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… RoBuST “has been developed as root and bulb plant community research platform for integrated analysis of [...]
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 [...]
RCSB has put goether a PDB Comparison Tool Widget . I put in 2K9G and 1ZLM, two SH3 domains. Used chain A for both and blast2seq as comparison algorithm (there are several choices), and these are my results. I’m not promising any biological significance to my choices and results, but the widget works nicely and simply. [...]
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 [...]
Today’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 [...]
If you are a biomedical researcher, have you ever used protein databases like UniProt to get information about proteins that you are interested in? Do you know how that database got there? I don’t mean today, I mean decades ago—how did a resource like this come to even exist at all? When researchers search a [...]
This week’s tip introduces a nice feature and tool of the Viral Bioinformatics Resource Center (VBRC). There are a lot of great tools at the VBRC to search and analyze hundreds of viral genomes. Most, if not all, of the tools can be used for searching and analyzing bacterial genomes also. The tool we are [...]
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