Massive sequence comparisons as a help in annotating genomic sequences.
An all-by-all comparison of all the publicly available protein sequences from plants has been performed, followed by a clusterization process. Within each of the 1064 resulting clusters-containing sequences that are orthologous as well as paralogous-the sequences have been submitted to a pyramidal classification and their domains delineated by an automated procedure à la. This process provides a means for easily checking for any apparent inconsistency in a cluster, for example, whether one sequence is shorter or longer than the others, one domain is missing, etc. In such cases, the alignment of the DNA sequence of the gene with that of a close homologous protein often reveals (in 10% of the clusters) probable sequencing errors (leading to frameshifts) or probable wrong intron/exon predictions. The composition of the clusters, their pyramidal classifications, and domain decomposition, as well as our comments when appropriate, are available from http://chlora.infobiogen.fr:1234/PHYTOPROT.
Louis
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A
Laboratoire Génome et Informatique, Université de Versailles, 78035 Versailles Cedex, France. louis@genetique.uvsq.fr
Ollivier
E
E
Aude
J C
JC
Risler
J L
JL
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D018745:Genome, Plant; D007770:L-Lactate Dehydrogenase / Q000235:genetics; D008291:Malate Dehydrogenase / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D010940:Plant Proteins / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods; D017386:Sequence Homology, Amino Acid
D010940:Plant Proteins; D007770:L-Lactate Dehydrogenase; D008291:Malate Dehydrogenase