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COMPSEQ application details page
Counts the composition of dimer/trimer/etc words in a sequence
This takes a specified length of sequence and counts the number ofdistinct subsequences of that length that there are in the inputsequence(s). It can read in the result of a previous compseq analysis and use thisto set the expected frequencies of the subsequences. Unless you tell 'compseq' otherwise, it expects each word to be equallylikely. The 'Expected' frequency therefore of any dimer is 1/16 - thisis 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. Obviously this is not the case in real sequences - there will be bias infavour of some words. Compseq cannot otherwise guess what the 'Expected' frequency is. Youcan, however, tell it what the Expected frequencies are by givingcompseq the output of the analysis of another set of sequences, producedby a previous compseq run. So you take a set of sequences that are representative of the type ofsequence you expect and you run compseq on it to get your expectedsequence frequencies. You then take the sequences you wish to investigate, run compseq on themgiving compseq the expected frequencies that you have established,above. You tell compseq what the file of expected frequencies is byspecifying it with '-infile filename' on the command-line.
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