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A cacophony of comparative genomics papers

By Jason Stajich, on September 14th, 2009

A nice series of comparative genomics articles have been published in the last few weeks. The pace of genome sequencing has accelerated to the point that we have lots of sequencing projects coming from individual labs and small consortia not necessarily from genome centers. We are seeing a preview of what next (2nd) generation [...]

September 14th, 2009 | Tags: , , , , , , , | Category: animal pathogen, candida, comparative, filamentous, genome sequencing, pezizomycota, saccharomyces, short-read, zygomycete | Leave a comment

Yeast population genomics

By Jason Stajich, on March 1st, 2009

ResearchBlogging.org
I cheered the Sanger-Wellcome SGRP group work to generate multiple Saccharomyces cerevisiae and S. paradoxus strain genome sequences. They submitted a version of the manuscript to Nature precedings and it is now published in Nature AOP showing that submitting to a preprint server doesn’t necessarily hurt your manuscript getting published in this instance. The research groups explored the impact of domestication (as was also recently done for the sake and soy sauce worker fungus, Aspergillus oryzae) on the Saccharomyces genome by comparing individuals from wild strains of S. [...]

March 1st, 2009 | Tags: , , , , , | Category: SGRP, bioinformatics, comparative, genome annotation, population genomics, resequencing, saccharomyces, short-read | Leave a comment

Lichen genome projects and the power shift prompted by next-gen sequencing

By Jason Stajich, on October 31st, 2008

Genome Technology highlights the very cool thing about next-gen sequencing – it puts the power in the hands of the researchers to explore genome sequence and doesn’t limit them to projects only funded through sequencing centers. The Genome Technology piece highlights work at Duke to sequence the genome Cladonia grayi, a lichenized fungus, with 454 technology at Duke’s Institute for Genome Sciences and Policy through their next-gen sequencing program. [...]

October 31st, 2008 | Tags: , , , , , , , , | Category: bioinformatics, comparative, genome annotation, short-read, symbiosis | One comment

Fungal genome assembly from short-read sequences

By Jason Stajich, on June 16th, 2008

This is a research blog so I though I’d post some quick numbers we are seeing for de novo assembly of the [[Neurospora crassa]] genome using Velvet. The genome of N.crassa is about 40Mb and sequencing of several flow cells using Solexa/Illumina technology to see what kind of de novo reconstruction we’d get. [...]

June 16th, 2008 | Tags: , , , , , | Category: bioinformatics, neurospora, resequencing, short-read | 8 comments