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PAVE: program for assembling and viewing ESTs.

Carol Soderlund1, Eric Johnson, Matthew Bomhoff

  • 1BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA. cari@agcol.arizona.edu

BMC Genomics
|August 28, 2009
PubMed
Summary
This summary is machine-generated.

The PAVE assembler improves transcript assembly by utilizing mate-pair information and efficiently handling 454 sequencing data. This program aids in creating more accurate contigs from both Sanger and 454 ESTs.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Emerging sequencing technologies like 454 Life Science present new challenges for EST assembly.
  • Traditional methods often fail to fully utilize mate-pair information, leading to fragmented contigs.
  • High-throughput sequencing generates large datasets that pose time and space constraints for assembly.

Purpose of the Study:

  • To develop an assembler that effectively integrates Sanger and 454 EST data.
  • To leverage 5' and 3' mate-pair information for improved contig assembly.
  • To address the computational challenges of high-throughput sequencing data.

Main Methods:

  • The PAVE (Program for Assembling and Viewing ESTs) assembler was developed.
  • It enforces mate-pair constraints, joining sub-contigs with 'n's if they don't overlap.
  • Similar ESTs are 'buried' to retain expression data and manage large datasets, using MegaBLAST and CAP3.

Main Results:

  • PAVE successfully assembles Sanger and 454 ESTs, improving contig accuracy by using mate-pair information.
  • The 'burying' method effectively handles 454 data depth, preserving expression levels and overcoming space/time issues.
  • A data management system with a MySQL database and a Java viewer facilitate analysis and visualization.

Conclusions:

  • PAVE offers a robust solution for assembling ESTs from diverse sequencing platforms.
  • The software package includes assembly, data management, and visualization tools.
  • PAVE is freely available, promoting its adoption in research laboratories.