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Old 01-30-2015, 05:42 AM   #1
Location: Europe

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Default BLASTing masssive protein sequences


I have a transcriptome which consists of 38,000 protein sequences. Is it possible to BLAST all of them and find othologs and of these proteins and GeneOnology and pathways involved if there is any for these proteins.

Kindly guide me

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Old 01-31-2015, 01:09 PM   #2
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It is certainly possible to do the BLASTing.

Question is do you have access to a cluster/adequate hardware and patience, since this will likely take a while to complete. Based on the number of proteins I assume this is a eukaryotic (non-model?) organism. If there is a closely related genome/proteome available then you could significantly narrow your search space and speed up BLAST part.
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Old 01-31-2015, 01:21 PM   #3
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Hi GenoMax,

Thank you very much for your reply. Yes the organism in which I am working is a eukaryotic non-model organism. I know an organism called "Schistosoma mansoni" is a closely related organism which has genome in NCBI.

I have desktop system which has 256 GB RAM and 16 cores. How long will it take to BLAST the 68000 nucleotides sequence against database and filter out top3-5 homologs and their corresponding Gene Ontology or pathways?
Kindly guide me
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Old 01-31-2015, 03:03 PM   #4
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I would check this answer and try the Diamond BLASTx option as that will be the quickest route with similar results as NCBI BLAST/BLAST+.

Link to something similar:

All the best.
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Old 02-02-2015, 07:06 AM   #5
Rick Westerman
Location: Purdue University, Indiana, USA

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While Diamond is much faster than BlastX the results are different in that correspondence between the top hit from each program is likely to not be the same. I *think* that this is due to differences in determining the evalues. Digging deeper and taking, say, the top 10 hits will start showing similarities between the programs. This is not to say that Diamond's results are biologically incorrect but you do have to be aware that the programs are not drop-in replacements for each other.
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Old 02-17-2015, 08:04 PM   #6
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It's a pretty big job you're talking about because blastx is exceedingly slow and the data for annotating GOs is also rather cumbersome. For this reason we launched a cloud service which does this task quickly and cheaply. As the previous reply mentioned regarding Diamond, our aligner is also not identical to blastx, but the annotation results are comparable.
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blastp, ncbi-blast, protein sequences, uniprot

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