PubServer

PubServer automates collection and analysis of publications associated with groups of homologous proteins to support literature-based functional annotation.

Key Features:

• Automated homolog identification and literature retrieval: PubServer employs PSI-Blast to identify homologous proteins and retrieves linked literature references from Entrez Protein database entries at NCBI.
• User-adjustable filtering criteria: It applies configurable filtering criteria to exclude publications unlikely to provide relevant insights.
• Vocabulary statistics and keyword identification: It generates vocabulary statistics and identifies frequent keywords from titles, abstracts, and MeSH terms.

Scientific Applications:

• Functional annotation: Analysis of publications linked to homologous protein sets supports functional annotation and refinement of protein families or individual genes.
• Literature-derived theme identification: Identification of common themes and frequent keywords across collected publications informs hypotheses about protein function.

Methodology:

PSI-Blast for homolog identification; retrieval of literature references from Entrez Protein database entries at NCBI; computation of vocabulary statistics from titles, abstracts, and MeSH terms; application of adjustable filtering criteria.