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Table 1 Comparison of different annotation pipelines

From: A comparative proteomics resource: proteins of Arabidopsis thaliana

Pipeline

Focus area

Applications

Coverage

GeneQuiz

Sequence homology

Function assignment

BLAST, FASTA, COILS,

MaxHom, Prosite, Blocks,

Predict Protein, Coils,

Transmembrane helix, CAST.

65 genomes

PEDANT

Gene prediction

Sequence homology

Function assignment

Fold assignment

BLAST, PSI-BLAST,

HMMER, PREDATOR,

Orpheus, BLIMPS, STRIDE.

133 complete genomes, 91 partial genomes

PAT

Sequence homology

Function assignment

Fold recognition

Structure prediction

WU-BLAST, PSI-BLAST,

123D, HMMER

103+ genomes, continuous expansion