Revseq

[Gary Williams, Tel 01223 494522]

The example of a standard FASTA input file is in:
http://www.emboss.org/Themes/SequenceExamples/fasta

The full set of input sequence formats is described in:
http://www.emboss.org/Themes/SequenceFormats.html#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
'reversed'
-osdirectory out		to specify the output directory

Run 'revseq -help -verbose' for further information.

Regards,
Gary


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