I am running BLAST search of a target gene in Staph. aureus to find interspecies gene similarity. The BLAST results (top 100) show the target gene in different strains of Staph. aureus. I downloaded the FASTA with all search results (>1000 sequence matches) but manually editing the FASTA is a cumbersome job. The phylogeny tree with this FASTA is a mess. Is there any software available which can cluster the sequences from a single organism into just one branch (no further branching for each strain as they have >99% sequence similarity) of the phylogeny tree so I can compare the similarity of target gene between Staph. aureus and other organisms.
A popular tool for that job is USEARCH with the algorithm UCLUST.
Please take a look here: http://drive5.com/usearch/manual/uclust_algo.html
I hope that helps. Best regards.
Dear Raman Sigh,
An alternative to the program mentioned by Salvador Ramirez-Flandes, and a general purpose clustering program is CD-HIT. It does not work with taxonomy information, but simply clusters sequences (nucleotides or proteins) based on coverage and similarity thresholds. It might solve your problem too.
I hope it helps.
Cheers.
JMC
True Joan.. did not know CD-HIT can be used to cluster nucleotide sequences too, which is why I did not recommended that tool (I have used that tool to cluster protein sequences only). However, I've checked the associated website and it seems that project isn't active anymore. Also, some problems in the CD-HIT algorithm have been reported (actually in the very same USEARCH article). But the problem with USEARCH is that only the 32bit version is free and that limits the number of sequences you can cluster. For Raman's question there is no problem since he is going to cluster at most hundreds of sequences, but when you have millions, then 32bits version of USEARCH cannot be used. There is, however, a project called VSEARCH (https://github.com/torognes/vsearch) which aims to be a free and unrestricted version of USEARCH.
Just saying this in case you might want to check it, Joan..
Best regards.
Article VSEARCH: A versatile open source tool for metagenomics
Dear Salvador and Joan,
Thank you very much for helpful inputs. This makes my life a bit easier!
@Raman, I have a tool that I made called HAQESAC (http://rest.slimsuite.unsw.edu.au/haqesac) that is designed for cleaning up messy gene families and getting rid of within-species variants and/or in-paralogues. It will also clean up the alignment a bit by chucking out badly-aligning sequences and can be run either interactively or non-interactively. It's built on BLAST(+). I'd be happy to help you get it running if the other solutions do not solve your problem. There's a wrapper (MultiHAQ) that let's you churn through multiple datasets if you have more than one.
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