Scientific Curator – Bioinformatics Interested individuals should apply on-line at www.jax.org/careers, referring to job posting #3256. Contact Jeannine Ross at ext. 6045 with questions. The incumbent in this position plays a critical role in data annotation and curation for the Gene Ontology (GO) and Protein Ontology (PRO) programs at The Jackson Laboratory in Bar Harbor [...]
Here is a study that looked for a type of genes that the authors felt was neglected by classic genomic annotation. The research shows how to employed concepts in molecular evolution to validate the existence of these genes. Some background: the first question we ask after assembling a genome is: “where are the genes”? Not [...]
NSF grant funded, woohoo! Now I am hiring a programmer. So if you want to be part of a dynamic, growing lab, do lots of interesting stuff and upgrade yourself from just a great bioinformatician to a super-bioinformatician, this job’s for you. You’ll be working primarily on microbial genome evolution, including setting up a kick-butt [...]
I just received an email from Julian Gough , one of last year’s CAFA participants. He started a Wikipedia initiative on protein function prediction, which are barely stubs at the moment. EDIT: He alerted me to the fact that protein function prediction has virtually no presence on Wikipedia. So all you protein function predictors out there, please contribute. Yes, [...]
If you have a merged file of paired-end reads, here is a quick way to read them using Biopython: from Bio import SeqIO from itertools import izip_longest # Loop over pairs of reads readiter = SeqIO.parse(open(inpath), “fastq”) for rec1, rec2 in izip_longest(readiter, readiter): print rec1.id # do something with rec1 print rec2.id # do something [...]
Good news: Press Release 2011-10-03 The Nobel Assembly at Karolinska Institutet has today decided that The Nobel Prize in Physiology or Medicine 2011 shall be divided, with one half jointly to Bruce A. Beutler and Jules A. Hoffmann for their discoveries concerning the activation of innate immunity and the other half to Ralph M. Steinman [...]
So you received your mate-paired reads in two different files, and you need to merge them for your assembler. Here is a quick Python script to do that. You will need Biopython installed. #!/usr/bin/env python from Bio import SeqIO import itertools import sys import os # Copyright(C) 2011 Iddo Friedberg # Released under Biopython [...]
The AFP/CAFA 2011 meeting was held on July 15 and July 16. Yes, it was a huge success, and I’m not just saying that beacuse I am one of the organizers. I will write up something more comprehensive soon; in the meantime, here are my tweets from the meeting. I am learning a lot about [...]
ISMB this year had quite a few twiterrers. Hashtag: #ISMB. I tried to collect all the #ISMB tweets, so I wrote my own twitter scavenger script, but it seems to go only 3 days back. I am not sure if this is a Twitter feature, or something with the library I am using (tweepy) or [...]
Nearly a year ago, I posted about the Critical Assessment of Function prediction with which I am involved. The original post from July 22, 2010 is in the block quote. After that, an update about the meeting which will be held in exactly 2 weeks. The trouble with genomic sequencing, is that it is too [...]
For some time now, NERC has been providing us with Bio-Linux. If you don’t want to be bothered with installing all the essential bioinformatic software for your Ubuntu box, you can install Bio-Linux, either as a a Linux distro for installation from scratch, or as a set of packages for an already existing Debian or Ubuntu [...]
Last July I introduced CAFA: Critical Assessment of (Gene and Protein) Function Annotations. Recap: the number of genomic and metagenomic sequences is growing at a horrendous rate. We are inundated with sequence data, yet the fraction of useful information we can glean from these sequences is steadily decreasing. There are simply too many sequences, and they are [...]
…you find this on the top of the paper pile on his desk:
I have just returned from British Columbia in Canada. I have to admit that their license plate motto is quite accurate: BC is incredibly beautiful. Another thing that struck me is the provincial flag of BC: the Union Jack at the top (OK, it is British Columbia), there are white and blue horizontal stripes, and [...]
