[EMBOSS] annotation

[Gary Williams, Tel 01223 494522]

Tom,

If you can change your list of matching IDs to a list of EMBOSS USAs,
then maybe somthing like the following might do what you require:


showfeat @list-of-your-ids -matchtag gene -values -pos -tag -stricttag
-width 0 -nodescription -noid -notype -out oputfile -auto

For example:
showfeat em:hsfau -matchtag gene -values -pos -tag -stricttag -width 0
-nodescription -noid -notype -auto stdout

57-458  gene="fau" 

Regards,
Gary


Thomas J Keller wrote:
> 
> Greetings,
> Could someone recommend an efficient way to get the annotation for the best hits from a blast search?
> In other words, if I run megablast and get back a list of matches with a cutoff e-value, what's a good way to get to get the gene name (if known) for the hit?
> 
> Thanks,
> Tom Keller
> 
> Thomas J. Keller, Ph.D.
> Director, MMI Core Facility
> Oregon Health & Science University
> 3181 SW Sam Jackson Park Rd.
> Portland, OR, USA, 97239
> 
> http://www.ohsu.edu/research/core

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk