NodProts database

Marta Matvienko matvienko at 2xtreme.net
Wed Oct 24 07:23:11 EST 2001

We are pleased to announce the NodProts Database.

Exploiting a number of bioinformatics tools, we have mapped publicly
available legume nodule protein sequences (nodulins) on the Arabidopsis
genome.  Some 760 nodulins have been searched against Arabidopsis
predicted ORFs, using the FASTA program.  The resulting set of legume
protein sequences and homologous Arabidopsis protein sequences have been
grouped into clusters, using the PhyloGrapher program.
We have identified 134 clusters of nodulins, with a significant level of
homology within each cluster (e < 0.0001; identity > 20%). For 29 of
these clusters, we have not found Arabidopsis homologues.  Arabidopsis
homologues for 105 clusters of legume nodulins have been drawn on
Arabidopsis chromosomes using the GenomePixelizer program.  To obtain a
visually readable picture of nodulin homologues on Arabidopsis
chromosomes, the total set of about 1250 Arabidopsis genes have been
divided into 7 separate groups.  Each group represents Arabidopsis
homologues of 13 to 15 clusters of nodulins.  The Arabidopsis genes are
web-linked to their legume homologues in GenBank, and to their protein
sequences in the MIPS database.  The mapping data, as well as the the
graph of nodulins lacking Arabidopsis homologues are presented in an
interactive format at http://www.intellectualforce.com/nodprots.shtml

Please address your comments and bug reports to Marta Matvienko at
nodprots at intellectualforce.com

Happy browsing,

Marta Matvienko
Intellectual Force
Davis, CA

info at intellectualforce.com


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