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Old 08-27-2015, 08:49 AM   #1
NYGen
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Default Looking for the right tool for very-distantly-related similarity search

Hello Seqanswers,

I need some help in deciding which tool (preferably web-based) is best for searching for very-distantly related homolog genes. I have a set of 100 human genes (all with nucleotide/protein refseqs) and Iím trying to find homologs in the model plant system Arabidopsis (I know, I know- but bear with me please). I realize that thereís going to be extreme divergence between sequences of homologs, if they even exist in the first place, but Iím willing to go on a wild goose chase if it means even a decent chance of finding a small subset of conserved genes.

Right now Iím just trying a few things with the first five accessions of interest. tBLASTx with a lenient matrix (blosum45 and trying pam250 now) did a good job finding some Arabidopsis genes with the same functional domain (e.g. zinc finger TF hits), but Iím learning that this isnít necessarily the best way to go about this search in species divergence above family/order levels of taxonomic differentiation... So, NCBIís help page recommends PSI-BLAST for distantly-related proteins, which Iím going to try next.

Iíve looked around seqanswers, biostars, and random pages via google, but mostly Iíve only turned up pages looking for faster BLAST alternatives, and speed isnít really a concern for me. I was at some point led to a page describing HMMER, which Iíve heard about but never used but apparently has a devoted server now at EBI. Is this likely to be a helpful resource for me?

Would walking up and down the phylogenetic tree be a worthwhile endeavor? I.e. search for homologs in well-documented models between human and Arabidopsis in a piecemeal system? Also, Iíve confirmed that none of my genes of interest are genes with a KOG/CEG designation, which would have been awesome.

Thanks for any guidance,
NYGen
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Old 08-27-2015, 09:59 AM   #2
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I've been reading NCBI's tutorial on PSI-BLAST and it's looking like the tool I should use. Other recommendations are of course welcome
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Old 08-27-2015, 10:09 AM   #3
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Look into Delta blast as a faster option: http://www.ncbi.nlm.nih.gov/pubmed/22510480
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Old 08-28-2015, 10:34 AM   #4
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Thanks a million for recommending DELTA-BLAST; that was absolutely what I needed. Also, legitimately cool paper. Cheers
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