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Related Experiment Videos

SledgeHMMER: a web server for batch searching the Pfam database.

Giridhar Chukkapalli1, Chittibabu Guda, Shankar Subramaniam

  • 1San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA.

Nucleic Acids Research
|June 25, 2004
PubMed
Summary
This summary is machine-generated.

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SledgeHMMER offers genome-scale Pfam database searches via a web server, eliminating local software installation. It efficiently processes batch sequences, providing results via email.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The Pfam database is a comprehensive collection of protein families, crucial for protein sequence analysis and annotation.
  • Local installation of the HMMER software and Pfam database can be resource-intensive and complex for users.
  • Genome-scale analysis requires efficient and accessible tools for searching large sequence datasets against protein family databases.

Purpose of the Study:

  • To provide a user-friendly web server for genome-scale searching of the Pfam database.
  • To enable users to perform Pfam searches without local installation of the HMMER software and Pfam database.
  • To offer efficient processing of batch sequences for large-scale protein family identification.

Main Methods:

  • Implementation of a parallelized version of the hmmpfam program for accelerated searching.

Related Experiment Videos

  • Pre-calculation of Pfam search results for large sequence databases (Swiss-Prot and TrEmbl) on high-performance computing resources.
  • A two-stage search process: matching against pre-calculated entries, followed by a new search for non-matching sequences.
  • Support for local, glocal, and merged search modes with gathering or E-value thresholds.
  • Batch processing of an unlimited number of query sequences.

    • Main Results:

    • The SledgeHMMER web server successfully performs genome-scale Pfam searches.
    • Pre-calculated results for approximately 1.2 million sequences in Swiss-Prot and TrEmbl are available.
    • The server efficiently handles batch queries without sequence number limitations.
    • Search results are delivered via email in a tabular format.

    Conclusions:

    • SledgeHMMER provides a valuable, accessible resource for large-scale protein family analysis.
    • The web server simplifies the process of searching the Pfam database, benefiting researchers without local infrastructure.
    • The ability to process unlimited batch sequences significantly enhances throughput for genomic studies.