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Organizing and Updating Whole Genome BLAST Searches with ReHAB

  • David J Esteban
  • Aijazuddin Syed
  • Chris Upton
Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)

Summary

In the current genomics era, protein and DNA sequence databases are continuously growing at an exponential rate. It has become increasingly important and useful to repeat similarity searches at frequent intervals, which then retrieve larger and larger sets of results. In addition, sequence similarity searches are now often performed with many sequences or even whole genomes. ReHAB (Recent Hits Acquired from Basic Local Alignment Search Tool [BLAST]) is a tool for tracking new protein hits in repeated PSI-BLAST searches. It is designed to simplify the analysis of large numbers of database matches and is therefore especially suited to comparative genomics. Results are presented in a user-friendly graphical interface with simple-to-navigate tables and new hits are indicated by highlighted text. In this paper, we describe the use of this software for organizing results from whole virus genome PSI-BLAST searches using a ReHAB database maintained at the Virus Bioinformatics Resource Centre.

Key Words

ReHAB BLAST genomics virus bioinformatics database PSI-BLAST similarity searches VBRC 

Notes

Acknowledgments

Thanks to Angelika Ehlers for assistance with programming and Cristalle Watson for assistance with editing the manuscript.

References

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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • David J Esteban
    • 1
  • Aijazuddin Syed
    • 2
  • Chris Upton
    • 3
  1. 1.Department of Biochemistry & MicrobiologyUniversity of VictoriaBritish Columbia, CANADA
  2. 2.Department of Biochemistry & MicrobiologyUniversity of VictoriaBritish Columbia, CANADA
  3. 3.Department of Biochemistry & MicrobiologyUniversity of VictoriaBritish Columbia, CANADA

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