CoSMoS: Conserved Sequence Motif Search in the proteome.
BACKGROUND
With the ever-increasing number of gene sequences in the public databases, generating and analyzing multiple sequence alignments becomes increasingly time consuming. Nevertheless it is a task performed on a regular basis by researchers in many labs.


RESULTS
We have now created a database called CoSMoS to find the occurrences and at the same time evaluate the significance of sequence motifs and amino acids encoded in the whole genome of the model organism Escherichia coli K12. We provide a precomputed set of multiple sequence alignments for each individual E. coli protein with all of its homologues in the RefSeq database. The alignments themselves, information about the occurrence of sequence motifs together with information on the conservation of each of the more than 1.3 million amino acids encoded in the E. coli genome can be accessed via the web interface of CoSMoS.


CONCLUSIONS
CoSMoS is a valuable tool to identify highly conserved sequence motifs, to find regions suitable for mutational studies in functional analyses and to predict important structural features in E. coli proteins.
Liu
Xiao I
XI
Department of Molecular, Cellular & Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA. catqliu@umich.edu
Korde
Neeraj
N
Jakob
Ursula
U
Leichert
Lars I
LI
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D004252:DNA Mutational Analysis; D030562:Databases, Protein; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics*; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D020407:Internet; D008969:Molecular Sequence Data; D011506:Proteins; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D016415:Sequence Alignment; D017421:Sequence Analysis; D017386:Sequence Homology, Amino Acid; D012984:Software; D013879:Thioredoxins / Q000378:metabolism; D013997:Time Factors
D029968:Escherichia coli Proteins; D011506:Proteins; D020543:Proteome; D013879:Thioredoxins