CBCB at UM
Chris Burge's lab
Chris Lee's lab
M. Zhang's lab
The Black lab
Genefinding on Yahoo!
Yi Xing's blog
Steve Mount's blog
email - Steve Mount
This is Steve Mount's web page for gene annotation and splice site
selection. The page was inspired by my review article in the American Journal of Human Genetics (PubMed; Journal)
I provide links on gene annotation (including cDNA alignment), genefinding, splicing signals (including splice site prediction), and specific comments on splice site consensus, ESEs and microexons. These pages, collectively accessible as www.RNAinfo.org, are a bit out of date right now (April, 2005) but under active revision.
Gene annotation incorporates cDNA data (including ESTs); sequence
similarity; and computational predictions based on the recognition of
probable splice sites and coding regions. The state of the art was recently
surveyed by the Gene Annotation Assessment Project (GASP1), the results of
which were published in a special issue of Genome
Ensembl - Ensembl
is a joint project between EMBL-EBI and the Sanger Centre to develop a
software system which produces and maintains automatic annotation on
Consortium - The goal of the Gene Ontology Consortium is to
produce a dynamic controlled vocabulary that can be applied to all
eukaryotes even as knowledge of gene and protein roles in cells is
accumulating and changing.
National Laboratory Computational Biosciences Section - A project
whose stated mission is to address fundamental questions in the life
sciences and provide information and analytical resources to the wider
biology research community.
TIGR Databases - The
Institute for Genomic Research TIGR Databases are a collection of curated
databases containing DNA and protein sequence, gene expression, cellular
role, protein family, and taxonomic data for microbes, plants and
Celera genomics, a division of PE Corporation, which produced the fruit
fly and human genomes. They are currently working on the mouse, and have
announced a plan to move into proteomics.
SIM4 - SIM4
is described by
Florea et al..
Intronerator - a collection of tools for exploring the molecular
biology and genomics of C. elegans with a special emphasis on alternative
splicing. This is specific to C. elegans, and does more than align
A list of selected documented microexons
is available. Very small exons, or microexons, pose special problems for
gene annotation. They are difficult to recognize using computational
genefinding methods, and can even confound the alignment of cDNA and
genomic sequences. Furthermore, because microexons are very often the
of alternative splicing, an understanding of how they are recognized
regulated) is key to understanding gene expression.