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Ballast: blast post-processing based on locally conserved segments.

F Plewniak1, J D Thompson, O Poch

  • 1Institut de Génétique et de Biologie Moléculaire et Cellulaire, Laboratoire de Biologie Structurale, (CNRS/INSERM/ULP), BP 163, 67404 Illkirch Cedex, France. plewniak@igbmc.u-strasbg.fr

Bioinformatics (Oxford, England)
|December 8, 2000
PubMed
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Ballast identifies conserved segments in protein sequences, improving the detection of distantly related homologs missed by BLAST. This tool enhances sequence similarity searches by highlighting divergent evolutionary relationships.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • BLAST is effective for strong sequence similarities but struggles with distant homologs, assigning them low ranks.
  • Divergent homologs often possess conserved segments (local maximum segments) that are crucial for evolutionary analysis.

Purpose of the Study:

  • To develop Ballast, a program for predicting local maximum segments (LMSs) from BLAST searches.
  • To highlight divergent protein homologs that may be missed by standard BLAST analysis.

Main Methods:

  • Ballast predicts LMSs from single BLAST database searches, utilizing conserved regions within sequences.
  • It can process TBlastN searches using information from joint BlastP searches.
  • The algorithm was applied to well-characterized protein families (aminoacyl-tRNA synthetases, helicases) against the SwissProt 38 database.

Related Experiment Videos

Main Results:

  • Ballast successfully builds conservation profiles and predicts LMSs consistent with known signatures and motifs.
  • LMSs provide a superior scoring scheme for ranking distant homologs compared to BLAST and PsiBlast.
  • A web-based graphical user interface allows selection of specific LMSs for detecting divergent homologs.

Conclusions:

  • Ballast effectively identifies conserved segments to reveal distantly related protein homologs.
  • The tool enhances sequence similarity searches by improving the detection and ranking of divergent evolutionary relationships.
  • Ballast offers a valuable method for exploring evolutionary connections beyond standard BLAST capabilities.