Tag Archives: alignments

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

VISTA, genome comparison resource

The VISTA comparative genome analysis resource updated their interface a few months ago. Additionally, they’ve added VISTA-Point (which replaces and greatly extends VISTA text browser) which, as the site says, allows the user to:

Access complete data and visual presentation of pairwise and multiple alignments of whole genome assemblies.

The homepage has undergone a very nice redesign. Much of the underlying VISTA browser and other tools functionality and use is similar (though updated of course). We understand also that there will be upcoming updates to some tools and the addition of others. Look for that here :D.

Also, we’ve updated our tutorial to reflect the new site and functions. As before, this tutorial is free to users and sponsored by VISTA. Check it out.

COBALT

I have a vague memory of reading about COBALT a while back, but at the time it was an executable file to download and I think I put it away as “to do.”  Well, a couple days ago I was over at the NCBI BLAST site for something (tip of the week?), and noticed there was a “new” flash for COBALT. So, COBALT is now integrated as a web-tool on the NCBI site. The short description of what COBALT is, from the site:

COBALT is a multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST.
Pairwise constraints are then incorporated into a progressive multiple alignment.

I haven’t tried it out yet, compared it to other multiple sequence alignment tools, but thought I’d point it out to those who haven’t yet noticed it.

Tip of the Week: TARGeT

target_thumbToday’s tip is on a TARGeT. TARGeT is, as the the paper’s title in the this year’s NAR’s issue states, “a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences.” There are several things you can do at TARGeT. Using BLAST, PHI BLAST, MUSCLE and TreeBest ,the main function of TARGeT is  to quickly obtain gene and transposon families from a query sequence. The tip today is a quick intro to the tool and a search on an R1 non-LTR transposon.