Question: Blastp in matlab
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gravatar for niloofaraghaie
3.1 years ago by
niloofaraghaie0 wrote:

Hello As novice in bioinformatics,I have a problem with blast algorithm in order to implement in matlab. I have 32 genomes and I want to find ortholog genes using blastp. However, as I see matlab as well as NCBI blast algorithm I cannot find any solution. In fact, I do not how to run blastp, create local NCBI database, and ... . My main point is to make pairwise aligment between each two genes from different 32 genomes and find the orthologs. I would be grateful if someone gives a short example of how to run this module. Considerinf two genomes from ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/Staphylococcus_aureus_MRSA252_uid57839/ and ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/Staphylococcus_aureus_MSSA476_uid57841/ can anyone give me a sample of code in matlab? Thank you in advance

blast matlab ortholog genes • 1.1k views
ADD COMMENTlink written 3.1 years ago by niloofaraghaie0

If you need to work in Matlab then you are best off contacting their technical support.

If you are able to work on command line then you can follow NCBI's command line handbook for blast here.

ADD REPLYlink written 3.1 years ago by genomax70k

Just curious, but why do you need to reimplement this in Matlab? There are lots of tools and databases available to do this.

ADD REPLYlink written 3.1 years ago by Chris Fields2.1k
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