[metagenomics-jclub] meeting time & metagenomic short read gene predictor

[Adina Chuang Howe]

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
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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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