Gary Williams, Tel 01223 494522
gwilliam at hgmp.mrc.ac.uk
Mon Apr 7 10:04:42 UTC 2003
The example of a standard FASTA input file is in:
The full set of input sequence formats is described in:
To reverse and complement a set of sequences that are in separate FASTA
files, for example '*.seq'
revseq '*.seq' result.seq
This writes the results to a single file holding many sequences.
Note that you should put the *.seq in quote marks if you specify it on
the command line to stop the shell trying to expand the '*' for you.
I prefer to output a set of sequences like this to a single file,
because the resulting file name is then known and can be handled easily
by scripts, but you may need to run non-EMBOSS programs on the results
which might not be able to read in a file containing many FASTA format
sequences - they may require one sequence per file.
If you prefer to deal with many resulting sequence files, use the
qualifier '-ossingle' which will force the output sequence to be written
to individual files, each named using the ID name of the input sequence:
revseq '*.seq' result.seq -ossingle
You can specify other parts of the output file name using:
-osextension reversed to specify the extension name as
-osdirectory out to specify the output directory
Run 'revseq -help -verbose' for further information.
Sean.Maceachern at nre.vic.gov.au wrote:
> Hello, I am trying to reverse and compement a few hundred FASTA sequences
> and am having trouble getting the input files in the correct format. To
> date all I have as an example of an inputfile is a sequence entry that is
> in the example nucleic acid database 'tembl' format.
> If anyone could suggest the best way to reverse and complement a number of
> FASTA files or could show me an example of an input file it would be
> greatly appreciated.
> Thank you
> Sean MacEachern
> PhD Student
> Sean.Maceachern at nre.vic.gov.au
Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK
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