Hello, find a sequence in multifasta files

[tarteaga96]

I'm a Mol Biol resercher and I'm new handling sequences. I need to find sequences of specific genes in a multifasta file from Roche 454. How can I do it?. Is there software for this under Windows? Thaks

[GenoMax]

Simplest way would be to use the "blast 2 sequences" tool from NCBI Blast search page. Go to http://blast.ncbi.nlm.nih.gov/ and then scroll down to "Specialized BLAST" section.

Select Align two (or more) sequences using BLAST (bl2seq). Both sequence files will need to be in the multi-fasta format though. You could also provide accession numbers, GI # for the genes you are looking for instead of the actual sequence.

[tarteaga96]

Thanks, now I'm doing that, but it is very slow and we prefer perform alignments in a local machine. Is this possible in a Win platform?

[dariober]

Hello,

If you can handle a bit the command line, I think the minimal number of steps to run blast locally are:

1- Download blast executables for your system from
ftp://ftp.ncbi.nlm.nih.gov/blast/exe...blast+/LATEST/

2- Move to the directory where you have the executables. Prepare database of your 454 sequences (e.g. multifasta454.fa). On windows it could be something like

cd "C:/Program Files/blast+/ncbi-blast-2.2.26+/bin/"
makeblastdb -in path/to/multifasta454.fa -dbtype nucl

3- Blast your query file (genes) against the database above

blastn -query path/to/query.fa -db path/to/multifasta454.fa -out path/to/myoutput.blastout

Blastn has a lot of options for fine tuning how you want to find matches and how to report results.

Hope this helps

Dario

[tarteaga96]

Thank you Dario, I'll try.