
                                  compseq 



Function

   Calculate the composition of unique words in sequences

Description

   compseq calculates the composition of words of a specified length
   (dimer, trimer etc) in the input sequence(s). The word length is
   user-specified. The unique sequences (words), their observed count,
   observed frequency, expected frequency and (observed / expected)
   frequency are written to the output file. The (observed / expected)
   frequency highlights any words with unusually high (or low) occurence
   in the input sequences.

Algorithm

   By default, compseq makes the (false) assumption that each word is
   equally likely. The expected frequency therefore of any dimer is 1/16
   - this is simply the inverse of the number of possible dimers (AA, AC,
   AG, AT, CA, CC, CG, CT, GA, GC, GG, GT, TA, TC, TG, TT). Similarly,
   the expected frequency of any trimer is 1/64, etc. Clearly this is not
   the case in real sequences where there will be bias in favour of some
   monomers and words. There are ways around this (see "Notes").

   The normal behaviour of compseq is to count the frequencies of all
   words that occur by moving a window of length 'word' up by one each
   time. The '-frame' option allows you to move the window up by the
   length of the word each time, skipping over the intervening words. You
   can count only those words that occur in a single frame of the word by
   setting this value to a number other than zero. If you set it to 1 it
   will only count the words in frame 1, 2 will only count the words in
   frame 2 and so on.

Usage

   Here is a sample session with compseq

   To count the frequencies of dinucleotides in a file:


% compseq tembl:x65923 -word 2 result3.comp 
Calculate the composition of unique words in sequences

   Go to the input files for this example
   Go to the output files for this example

   Example 2

   To count the frequencies of hexanucleotides, without outputting the
   results of hexanucleotides that do not occur in the sequence:


% compseq tembl:x65923 -word 6 result6.comp -nozero 
Calculate the composition of unique words in sequences

   Go to the output files for this example

   Example 3

   To count the frequencies of trinucleotides in frame 2 of a sequence
   and use a previously prepared compseq output to show the expected
   frequencies:


% compseq tembl:x65923 -word 3 result3.comp -frame 2 -in prev.comp 
Calculate the composition of unique words in sequences

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -word               integer    [2] This is the size of word (n-mer) to
                                  count.
                                  Thus if you want to count codon frequencies,
                                  you should enter 3 here. (Integer from 1 to
                                  20)
  [-outfile]           outfile    [*.compseq] This is the results file.

   Additional (Optional) qualifiers (* if not always prompted):
   -infile             infile     This is a file previously produced by
                                  'compseq' that can be used to set the
                                  expected frequencies of words in this
                                  analysis.
                                  The word size in the current run must be the
                                  same as the one in this results file.
                                  Obviously, you should use a file produced
                                  from protein sequences if you are counting
                                  protein sequence word frequencies, and you
                                  must use one made from nucleotide
                                  frequencies if you are analysing a
                                  nucleotide sequence.
   -frame              integer    [0] The normal behaviour of 'compseq' is to
                                  count the frequencies of all words that
                                  occur by moving a window of length 'word' up
                                  by one each time.
                                  This option allows you to move the window up
                                  by the length of the word each time,
                                  skipping over the intervening words.
                                  You can count only those words that occur in
                                  a single frame of the word by setting this
                                  value to a number other than zero.
                                  If you set it to 1 it will only count the
                                  words in frame 1, 2 will only count the
                                  words in frame 2 and so on. (Integer 0 or
                                  more)
*  -[no]ignorebz       boolean    [Y] The amino acid code B represents
                                  Asparagine or Aspartic acid and the code Z
                                  represents Glutamine or Glutamic acid.
                                  These are not commonly used codes and you
                                  may wish not to count words containing them,
                                  just noting them in the count of 'Other'
                                  words.
*  -reverse            boolean    [N] Set this to be true if you also wish to
                                  also count words in the reverse complement
                                  of a nucleic sequence.
   -calcfreq           boolean    [N] If this is set true then the expected
                                  frequencies of words are calculated from the
                                  observed frequency of single bases or
                                  residues in the sequences.
                                  If you are reporting a word size of 1
                                  (single bases or residues) then there is no
                                  point in using this option because the
                                  calculated expected frequency will be equal
                                  to the observed frequency.
                                  Calculating the expected frequencies like
                                  this will give an approximation of the
                                  expected frequencies that you might get by
                                  using an input file of frequencies produced
                                  by a previous run of this program. If an
                                  input file of expected word frequencies has
                                  been specified then the values from that
                                  file will be used instead of this
                                  calculation of expected frequency from the
                                  sequence, even if 'calcfreq' is set to be
                                  true.
   -[no]zerocount      boolean    [Y] You can make the output results file
                                  much smaller if you do not display the words
                                  with a zero count.

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   Normal sequence(s) USA.

  Input files for usage example

   'tembl:x65923' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:x65923

ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC   X65923;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-518
RX   PUBMED; 8395683.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   H-InvDB; HIT000322806.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /organism="Homo sapiens"
FT                   /chromosome="11q"
FT                   /map="13"
FT                   /mol_type="mRNA"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /tissue_type="placenta"
FT                   /db_xref="taxon:9606"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /gene="fau"
FT                   /db_xref="GDB:135476"
FT                   /db_xref="GOA:P35544"
FT                   /db_xref="GOA:P62861"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLA
G
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKT
G
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        6
0
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       12
0
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       18
0
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       24
0
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       30
0
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       36
0
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       42
0
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       48
0
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               51
8
//

  Input files for usage example 3

  File: prev.comp

#
# Output from 'compseq'
#
# The Expected frequencies are calculated on the (false) assumption that every
# word has equal frequency.
#
# The input sequences are:
#       HSFAU


Word size       3
Total count     516

#
# Word  Obs Count       Obs Frequency   Exp Frequency   Obs/Exp Frequency
#
AAA     17              0.0329457       0.0156250       2.1085271
AAC     5               0.0096899       0.0156250       0.6201550
AAG     18              0.0348837       0.0156250       2.2325581
AAT     4               0.0077519       0.0156250       0.4961240
ACA     5               0.0096899       0.0156250       0.6201550
ACC     6               0.0116279       0.0156250       0.7441860
ACG     2               0.0038760       0.0156250       0.2480620
ACT     7               0.0135659       0.0156250       0.8682171
AGA     12              0.0232558       0.0156250       1.4883721
AGC     7               0.0135659       0.0156250       0.8682171
AGG     16              0.0310078       0.0156250       1.9844961
AGT     10              0.0193798       0.0156250       1.2403101
ATA     2               0.0038760       0.0156250       0.2480620
ATC     3               0.0058140       0.0156250       0.3720930
ATG     7               0.0135659       0.0156250       0.8682171
ATT     2               0.0038760       0.0156250       0.2480620
CAA     10              0.0193798       0.0156250       1.2403101
CAC     6               0.0116279       0.0156250       0.7441860
CAG     13              0.0251938       0.0156250       1.6124031
CAT     5               0.0096899       0.0156250       0.6201550
CCA     12              0.0232558       0.0156250       1.4883721
CCC     13              0.0251938       0.0156250       1.6124031
CCG     8               0.0155039       0.0156250       0.9922481
CCT     10              0.0193798       0.0156250       1.2403101
CGA     2               0.0038760       0.0156250       0.2480620
CGC     10              0.0193798       0.0156250       1.2403101
CGG     9               0.0174419       0.0156250       1.1162791
CGT     4               0.0077519       0.0156250       0.4961240
CTA     5               0.0096899       0.0156250       0.6201550
CTC     11              0.0213178       0.0156250       1.3643411
CTG     10              0.0193798       0.0156250       1.2403101
CTT     11              0.0213178       0.0156250       1.3643411
GAA     11              0.0213178       0.0156250       1.3643411
GAC     6               0.0116279       0.0156250       0.7441860
GAG     10              0.0193798       0.0156250       1.2403101
GAT     4               0.0077519       0.0156250       0.4961240
GCA     7               0.0135659       0.0156250       0.8682171
GCC     18              0.0348837       0.0156250       2.2325581
GCG     8               0.0155039       0.0156250       0.9922481
GCT     10              0.0193798       0.0156250       1.2403101
GGA     13              0.0251938       0.0156250       1.6124031
GGC     17              0.0329457       0.0156250       2.1085271
GGG     7               0.0135659       0.0156250       0.8682171
GGT     9               0.0174419       0.0156250       1.1162791
GTA     6               0.0116279       0.0156250       0.7441860
GTC     9               0.0174419       0.0156250       1.1162791
GTG     8               0.0155039       0.0156250       0.9922481
GTT     5               0.0096899       0.0156250       0.6201550
TAA     7               0.0135659       0.0156250       0.8682171
TAC     3               0.0058140       0.0156250       0.3720930
TAG     4               0.0077519       0.0156250       0.4961240
TAT     1               0.0019380       0.0156250       0.1240310
TCA     10              0.0193798       0.0156250       1.2403101
TCC     6               0.0116279       0.0156250       0.7441860
TCG     7               0.0135659       0.0156250       0.8682171
TCT     10              0.0193798       0.0156250       1.2403101
TGA     4               0.0077519       0.0156250       0.4961240
TGC     9               0.0174419       0.0156250       1.1162791
TGG     14              0.0271318       0.0156250       1.7364341
TGT     5               0.0096899       0.0156250       0.6201550
TTA     2               0.0038760       0.0156250       0.2480620
TTC     10              0.0193798       0.0156250       1.2403101
TTG     7               0.0135659       0.0156250       0.8682171
TTT     7               0.0135659       0.0156250       0.8682171

Other   0               0.0000000       0.0000000       10000000000.0000000

Output file format

   The output format consists of:

   Header information and comments are preceeded by a '#' character at
   the start of the line.

   The Word size and the Total count are then given on separate lines,

   The headers of the columns of results are preceeded by a '#'

   The results columns are: the sub-sequence word, the observed
   frequency, the expected frequency (which will be read from the input
   file if one is given, else it is a simple inverse of the number of
   words of the size specified that can be constructed), the ratio of the
   observed to expected frequency.

   After a blank line at the end, the results of 'Other' words is given -
   this is the number of words with a sequence which has IUPAC ambiguity
   codes or other unusual characters in.

  Output files for usage example

  File: result3.comp

#
# Output from 'compseq'
#
# The Expected frequencies are calculated on the (false) assumption that every
# word has equal frequency.
#
# The input sequences are:
#       X65923


Word size       2
Total count     517

#
# Word  Obs Count       Obs Frequency   Exp Frequency   Obs/Exp Frequency
#
AA      45              0.0870406       0.0625000       1.3926499
AC      20              0.0386847       0.0625000       0.6189555
AG      45              0.0870406       0.0625000       1.3926499
AT      14              0.0270793       0.0625000       0.4332689
CA      34              0.0657640       0.0625000       1.0522244
CC      43              0.0831721       0.0625000       1.3307544
CG      25              0.0483559       0.0625000       0.7736944
CT      37              0.0715667       0.0625000       1.1450677
GA      31              0.0599613       0.0625000       0.9593810
GC      43              0.0831721       0.0625000       1.3307544
GG      46              0.0889749       0.0625000       1.4235977
GT      28              0.0541586       0.0625000       0.8665377
TA      15              0.0290135       0.0625000       0.4642166
TC      33              0.0638298       0.0625000       1.0212766
TG      32              0.0618956       0.0625000       0.9903288
TT      26              0.0502901       0.0625000       0.8046422

Other   0               0.0000000       0.0000000       10000000000.0000000

  Output files for usage example 2

  File: result6.comp

#
# Output from 'compseq'
#
# Words with a frequency of zero are not reported.
# The Expected frequencies are calculated on the (false) assumption that every
# word has equal frequency.
#
# The input sequences are:
#       X65923


Word size       6
Total count     513

#
# Word  Obs Count       Obs Frequency   Exp Frequency   Obs/Exp Frequency
#
AAAAAA  6               0.0116959       0.0002441       47.9064327
AAAAAG  1               0.0019493       0.0002441       7.9844055
AAAAGC  1               0.0019493       0.0002441       7.9844055
AAAAGT  1               0.0019493       0.0002441       7.9844055
AAACAG  1               0.0019493       0.0002441       7.9844055
AAACGG  1               0.0019493       0.0002441       7.9844055
AAAGCC  1               0.0019493       0.0002441       7.9844055
AAAGTG  1               0.0019493       0.0002441       7.9844055
AAAGTT  1               0.0019493       0.0002441       7.9844055
AACAGG  1               0.0019493       0.0002441       7.9844055
AACCGG  1               0.0019493       0.0002441       7.9844055
AACGGT  1               0.0019493       0.0002441       7.9844055
AACGTT  1               0.0019493       0.0002441       7.9844055
AACTCT  1               0.0019493       0.0002441       7.9844055
AAGAAG  6               0.0116959       0.0002441       47.9064327
AAGACA  1               0.0019493       0.0002441       7.9844055
AAGATC  1               0.0019493       0.0002441       7.9844055
AAGCCA  1               0.0019493       0.0002441       7.9844055
AAGCGG  1               0.0019493       0.0002441       7.9844055
AAGGCT  1               0.0019493       0.0002441       7.9844055
AAGGGC  1               0.0019493       0.0002441       7.9844055
AAGGTG  1               0.0019493       0.0002441       7.9844055
AAGTAG  1               0.0019493       0.0002441       7.9844055
AAGTCG  1               0.0019493       0.0002441       7.9844055
AAGTCT  1               0.0019493       0.0002441       7.9844055
AAGTGA  1               0.0019493       0.0002441       7.9844055
AAGTTC  1               0.0019493       0.0002441       7.9844055
AATAAA  1               0.0019493       0.0002441       7.9844055
AATATG  1               0.0019493       0.0002441       7.9844055
AATGCC  1               0.0019493       0.0002441       7.9844055
AATTCT  1               0.0019493       0.0002441       7.9844055
ACAACC  1               0.0019493       0.0002441       7.9844055
ACACAC  1               0.0019493       0.0002441       7.9844055


  [Part of this file has been deleted for brevity]

TGAGGC  1               0.0019493       0.0002441       7.9844055
TGCAGC  1               0.0019493       0.0002441       7.9844055
TGCAGT  1               0.0019493       0.0002441       7.9844055
TGCCAA  1               0.0019493       0.0002441       7.9844055
TGCCCA  1               0.0019493       0.0002441       7.9844055
TGCCCC  1               0.0019493       0.0002441       7.9844055
TGCGGG  1               0.0019493       0.0002441       7.9844055
TGCTCC  1               0.0019493       0.0002441       7.9844055
TGCTGG  1               0.0019493       0.0002441       7.9844055
TGCTTG  1               0.0019493       0.0002441       7.9844055
TGGAAA  1               0.0019493       0.0002441       7.9844055
TGGAAG  1               0.0019493       0.0002441       7.9844055
TGGAGG  4               0.0077973       0.0002441       31.9376218
TGGCAA  1               0.0019493       0.0002441       7.9844055
TGGCAG  1               0.0019493       0.0002441       7.9844055
TGGCCA  1               0.0019493       0.0002441       7.9844055
TGGCCC  1               0.0019493       0.0002441       7.9844055
TGGCTT  1               0.0019493       0.0002441       7.9844055
TGGGAC  1               0.0019493       0.0002441       7.9844055
TGGGCC  1               0.0019493       0.0002441       7.9844055
TGGTTC  1               0.0019493       0.0002441       7.9844055
TGTAAT  1               0.0019493       0.0002441       7.9844055
TGTAGC  1               0.0019493       0.0002441       7.9844055
TGTCAA  1               0.0019493       0.0002441       7.9844055
TGTCCG  1               0.0019493       0.0002441       7.9844055
TGTGCC  1               0.0019493       0.0002441       7.9844055
TTAAGT  1               0.0019493       0.0002441       7.9844055
TTAGTT  1               0.0019493       0.0002441       7.9844055
TTCAGT  2               0.0038986       0.0002441       15.9688109
TTCATG  1               0.0019493       0.0002441       7.9844055
TTCCCT  1               0.0019493       0.0002441       7.9844055
TTCCTC  1               0.0019493       0.0002441       7.9844055
TTCGAG  1               0.0019493       0.0002441       7.9844055
TTCGCG  1               0.0019493       0.0002441       7.9844055
TTCTCG  1               0.0019493       0.0002441       7.9844055
TTCTCT  1               0.0019493       0.0002441       7.9844055
TTCTGG  1               0.0019493       0.0002441       7.9844055
TTGCCC  1               0.0019493       0.0002441       7.9844055
TTGGAG  1               0.0019493       0.0002441       7.9844055
TTGGCA  1               0.0019493       0.0002441       7.9844055
TTGTAA  1               0.0019493       0.0002441       7.9844055
TTGTCA  1               0.0019493       0.0002441       7.9844055
TTGTCC  1               0.0019493       0.0002441       7.9844055
TTGTGC  1               0.0019493       0.0002441       7.9844055
TTTCTC  2               0.0038986       0.0002441       15.9688109
TTTGGC  1               0.0019493       0.0002441       7.9844055
TTTGTA  1               0.0019493       0.0002441       7.9844055
TTTGTC  2               0.0038986       0.0002441       15.9688109
TTTTGT  1               0.0019493       0.0002441       7.9844055

Other   0               0.0000000       0.0000000       10000000000.0000000

  Output files for usage example 3

  File: result3.comp

#
# Output from 'compseq'
#
# Only words in frame 2 will be counted.
# The Expected frequencies are taken from the file: ../../data/prev.comp
#
# The input sequences are:
#       X65923


Word size       3
Total count     172

#
# Word  Obs Count       Obs Frequency   Exp Frequency   Obs/Exp Frequency
#
AAA     7               0.0406977       0.0329457       1.2352955
AAC     3               0.0174419       0.0096899       1.8000042
AAG     11              0.0639535       0.0348837       1.8333344
AAT     3               0.0174419       0.0077519       2.2500110
ACA     1               0.0058140       0.0096899       0.6000014
ACC     4               0.0232558       0.0116279       2.0000012
ACG     1               0.0058140       0.0038760       1.4999880
ACT     3               0.0174419       0.0135659       1.2857135
AGA     1               0.0058140       0.0232558       0.2500002
AGC     2               0.0116279       0.0135659       0.8571423
AGG     0               0.0000000       0.0310078       0.0000000
AGT     0               0.0000000       0.0193798       0.0000000
ATA     0               0.0000000       0.0038760       0.0000000
ATC     1               0.0058140       0.0058140       0.9999920
ATG     3               0.0174419       0.0135659       1.2857135
ATT     1               0.0058140       0.0038760       1.4999880
CAA     1               0.0058140       0.0193798       0.3000007
CAC     2               0.0116279       0.0116279       1.0000006
CAG     9               0.0523256       0.0251938       2.0769229
CAT     3               0.0174419       0.0096899       1.8000042
CCA     0               0.0000000       0.0232558       0.0000000
CCC     3               0.0174419       0.0251938       0.6923076
CCG     1               0.0058140       0.0155039       0.3749994
CCT     2               0.0116279       0.0193798       0.6000014
CGA     1               0.0058140       0.0038760       1.4999880
CGC     5               0.0290698       0.0193798       1.5000035
CGG     4               0.0232558       0.0174419       1.3333303
CGT     2               0.0116279       0.0077519       1.5000074
CTA     1               0.0058140       0.0096899       0.6000014
CTC     4               0.0232558       0.0213178       1.0909106
CTG     7               0.0406977       0.0193798       2.1000049
CTT     3               0.0174419       0.0213178       0.8181829
GAA     3               0.0174419       0.0213178       0.8181829
GAC     1               0.0058140       0.0116279       0.5000003
GAG     7               0.0406977       0.0193798       2.1000049
GAT     2               0.0116279       0.0077519       1.5000074
GCA     2               0.0116279       0.0135659       0.8571423
GCC     10              0.0581395       0.0348837       1.6666677
GCG     1               0.0058140       0.0155039       0.3749994
GCT     3               0.0174419       0.0193798       0.9000021
GGA     2               0.0116279       0.0251938       0.4615384
GGC     8               0.0465116       0.0329457       1.4117663
GGG     1               0.0058140       0.0135659       0.4285712
GGT     5               0.0290698       0.0174419       1.6666629
GTA     2               0.0116279       0.0116279       1.0000006
GTC     6               0.0348837       0.0174419       1.9999955
GTG     6               0.0348837       0.0155039       2.2499965
GTT     3               0.0174419       0.0096899       1.8000042
TAA     3               0.0174419       0.0135659       1.2857135
TAC     1               0.0058140       0.0058140       0.9999920
TAG     0               0.0000000       0.0077519       0.0000000
TAT     0               0.0000000       0.0019380       0.0000000
TCA     3               0.0174419       0.0193798       0.9000021
TCC     1               0.0058140       0.0116279       0.5000003
TCG     0               0.0000000       0.0135659       0.0000000
TCT     3               0.0174419       0.0193798       0.9000021
TGA     0               0.0000000       0.0077519       0.0000000
TGC     1               0.0058140       0.0174419       0.3333326
TGG     1               0.0058140       0.0271318       0.2142856
TGT     1               0.0058140       0.0096899       0.6000014
TTA     1               0.0058140       0.0038760       1.4999880
TTC     1               0.0058140       0.0193798       0.3000007
TTG     0               0.0000000       0.0135659       0.0000000
TTT     5               0.0290698       0.0135659       2.1428558

Other   0               0.0000000       0.0000000       10000000000.0000000

Data files

   The input data file is not required.

   The input data file format is exactly the same as the output file
   format.

   It expects to read in a previous output file of this program. An error
   is produced if the word size of the current compseq job and that of
   the output file being read in are different.

Notes

   There is no way for compseq to guess what the true expected frequency
   should be for each word. It can however read in the result of a
   previous compseq analysis and use this to set the expected frequencies
   of the subsequences. In this case, the input sequences under
   investigation should be representative of those used for the previous
   compseq analysis. It is down to your biological expertise to ensure
   the sequences are genuinely "representative", for instance, you might
   select a group of sequences belonging to the same taxonomic rank such
   as genus or species.

   The file of expected frequencies is specified by name with the -infile
   qualifier. The word size in the current run must be the same as the
   one in this results file. Obviously, you should use a file produced
   from protein sequences if you are counting protein sequence word
   frequencies, and you must use one made from nucleotide frequencies if
   you are analysing a nucleotide sequence.

   As an alternative to using -infile, the expected frequencies of words
   may be calculated from the observed frequency of single bases or
   residues in the sequences. To do this, specify the -calcfreq
   qualifier. If you are reporting a word size of 1 (single bases or
   residues) then there is no point in using this option because the
   calculated expected frequency will be equal to the observed frequency.

   Calculating the expected frequencies like this will give an
   approximation of the expected frequencies that you might get by using
   an input file of frequencies produced by a previous run of this
   program. If an input file of expected word frequencies has been
   specified then the values from that file will be used instead of this
   calculation of expected frequency from the sequence, even if
   'calcfreq' is set to be true.

References

   None.

Warnings

   The results are held in an array in memory before being written to a
   file. For large values of wordsize (over about 7 for nucleic, 5 for
   protein), you may run out of memory or generate a very large output
   file.

Diagnostic Error Messages

   "The word size is too large for the data structure available."
          You chose a word size that cannot be stored by the program.

   "Insufficient memory - aborting."
          You do not have enough memory - use a machine with more memory.

   "The word size you are counting (n) is different to the word size in
          the file of expected frequencies (n)."
          You chose different word sizes in the run of compseq that
          produced your results file used to display the expected word
          frequencies to the word size used in this run of compseq.

   "The 'Word size' line was not found, instead found:"
          You appear to be trying to read a corrupted compseq results
          file

Exit status

   It always exits with status 0 unless one of the above error conditions
   is found

Known bugs

   This program can use a large amount of memory is you specify a large
   word size (7 or above). This may impact the behaviour of other
   programs on your machine.

   If you run out of memory, you may see the program crash with a generic
   error message that will be specific to your machine's operating
   system, but will probably be a warning about writing to memory that
   the program does not own (eg "Segmentation fault" on a Solaris
   machine)

   This is not a bug, it is a feature of the way this program grabs large
   amounts of memory.

See also

   Program name Description
   backtranambig Back-translate a protein sequence to ambiguous
   nucleotide sequence
   backtranseq Back-translate a protein sequence to a nucleotide sequence
   banana Plot bending and curvature data for B-DNA
   btwisted Calculate the twisting in a B-DNA sequence
   chaos Draw a chaos game representation plot for a nucleotide sequence
   charge Draw a protein charge plot
   checktrans Reports STOP codons and ORF statistics of a protein
   dan Calculates nucleic acid melting temperature
   density Draw a nucleic acid density plot
   emowse Search protein sequences by digest fragment molecular weight
   freak Generate residue/base frequency table or plot
   iep Calculate the isoelectric point of proteins
   isochore Plots isochores in DNA sequences
   mwcontam Find weights common to multiple molecular weights files
   mwfilter Filter noisy data from molecular weights file
   octanol Draw a White-Wimley protein hydropathy plot
   pepinfo Plot amino acid properties of a protein sequence in parallel
   pepstats Calculates statistics of protein properties
   pepwindow Draw a Kyte-Doolittle hydropathy plot for a protein sequence
   pepwindowall Draw Kyte-Doolittle hydropathy plot for a protein
   alignment
   sirna Finds siRNA duplexes in mRNA
   wordcount Count and extract unique words in DNA sequence(s)

Author(s)

   Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

   Completed 2 March 2000
   5 April 2001 (version 1.12.0) - the operation of the option '-reverse'
   has changed. It is now 'False' by default instead of being 'True' by
   default for nucleic sequences. Too many people were getting confused
   by the counts being done on both senses, so this is now done on only
   the forward sense by default.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
