[metagenomics-jclub] Meeting next week 10/20/10, 930 AM, PSB 271

[Adina Chuang Howe]

There were some scheduling conflicts for this week.   So let's shoot for
next Wednesday.  We can talk about our assembly efforts then.

Hope to see you there,
Adina


On Sat, Oct 9, 2010 at 9:09 PM, Adina Chuang Howe <adina.chuang at gmail.com>wrote:

> hi all:
>
> let's try to have a meeting sometime in the next week or so.  is wednesday
> at 930 still ok for most folks this time around?  maybe we can talk a bit
> more about our graph traversal filter for assembly.
>
> adina
> -------
>
> FragGeneScan: predicting genes in short and
> error-prone reads
>
> ABSTRACT
> The advances of next-generation sequencing technology
> have facilitated metagenomics research that
> attempts to determine directly the whole collection
> of genetic material within an environmental sample
> (i.e. the metagenome). Identification of genes directly
> from short reads has become an important yet
> challenging problem in annotating metagenomes,
> since the assembly of metagenomes is often not
> available. Gene predictors developed for whole
> genomes (e.g. Glimmer) and recently developed for
> metagenomic sequences (e.g. MetaGene) show a
> significant decrease in performance as the
> sequencing error rates increase, or as reads get
> shorter. We have developed a novel gene prediction
> method FragGeneScan, which combines sequencing
> error models and codon usages in a hidden Markov
> model to improve the prediction of protein-coding
> region in short reads. The performance of
> FragGeneScan was comparable to Glimmer and
> MetaGene for complete genomes. But for short
> reads, FragGeneScan consistently outperformed
> MetaGene (accuracy improved 62% for reads of
> 400 bases with 1% sequencing errors, and 18%
> for short reads of 100 bases that are error free).
> When applied to metagenomes, FragGeneScan recovered
> substantially more genes than MetaGene
> predicted (>90% of the genes identified by
> homology search), and many novel genes with no
> homologs in current protein sequence database.
>
>
>
>
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