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Release Notes

Alpheus™ Sequence Variant Detection System

Software systems for DNA sequence variant discovery that are based upon Sanger chemistry and base calling algorithms are not optimal for next generation technologies that feature relatively deep coverage, short read lengths, novel base calling and quality score determination methods, and relatively high error rates1. The Alpheus™ Sequence Variant Detection System includes an automatic data handling module, a computational analysis pipeline, a results database and a web-based query and visualization interface. Alpheus™ has been designed and implemented as a software-as-a-service application. The software was designed to mine large DNA sequence datasets for variants meeting user-specified criteria, such as transcript abundance, positional coverage, variant frequencies, and putative variant functional properties. The web interface was created using Java J2EE technologies (servlets, JSP and JDBC), XML and Flash. The analysis pipeline was created using Java and uses parts of the BioJava BLAST parsing framework (http://biojava.org).

Version 2.3

  • Release date: February 15, 2008
  • Sample Comparison: Added ability to compare sequence variants found in genes across groups of samples.
  • Gene Expression: Added new search to enable finding genes by expression levels as measured by abundance of reads aligned to genes through either transcript or genomic alignments
  • Perfomance enhancements: Continued updates to queries and pipelining analysis to facilitate GigaBase scale experiments.

Version 2.2

  • Release date: April 30, 2007
  • ABI SOLiD data: Added ability to handle preliminary ABI SOLiD reads using alignments generated in color space by ABI alignment methods or in nucleotide space by GMAP or megaBLAST.
  • CCDS reference set: Added ability to use the Consensus CDS set as a transcript reference
  • Performance enhancements: Improved performance on pileup visualization and gene read coverage calculations

Version 2.1

  • Release date: April 12, 2007
  • Genomic Alignments: Genes and variants can be searched and visualized using alignments against a genomic reference.
  • Reference Data Loader: New module for loading genomic, transcript and variant reference data using files in GenBank Flat File format.
  • Homopolymer filter: New variant filter for hiding in/del variants that appear near a homopolymer region
  • Bug Fixes: Fixed GMAP identity count reporting bug
Known Issues
  • Pileup visualization close up view partially hides reads at the far 3' end
  • Transcript variants cannot be matched up with their genomic alignments
  • Genomic variants cannot be characterized by context (e.g. CDS, exon, intron)
  • Genomic variants cannot be characterized as non-synonymous SNPs
  • dbSNP reference data not incorporated for known genomic variants

Version 2.0

  • Release date: December 8, 2006
  • GMAP Alignments: Added the ability to use the GMAP2 alignment algorithm as well as megaBLAST3 for creating alignments of reads to a reference set.
  • Performance enhancements: Improved performance in many areas including querying and visualization.
  • Variant filtering: Added ability to filter variants by minimum and maximum % of reads that show variant. This enables searching for variants that are homozygous or heterozygous alleles.
  • Look and feel: New website look and feel along with ability to "plug and play" project specific templating elements
Known Issues
  • GMAP pairwise alignments report incorrect statistics for identity count and percent identity
  • Sequence data aligned with multiple algorithms must be processed as multiple samples


Alpheus™ Development Team

Alpheus™ was developed at the National Center for Genome Resources, Santa Fe, NM by:

  • Stephen F. Kingsmore, M.B., C.h.B., B.A.O
  • Neil Miller
  • Joann Mudge, Ph.D.
  • Andrew Farmer
  • Greg D. May, Ph.D.
  • Selene Virk
  • Kamal Gajendran
  • C. Forrest Black
  • M. Kathy Myers
  • Lar Mader
  • Dan Weems
  • Melodie Rice
  • Terri Gomez
  • Susan M. Baxter, Ph.D.
  • Sharon Lewis, M.D.
  • Steven Day
  • Linda Julien

Contact Us for more information about Alpheus™

1 Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005 437:376-80.
2 Wu TD, Watanabe CK. "GMAP: a genomic mapping and alignment program for mRNA and EST sequences", Bioinformatics 2005 May 1;21(9):1859-75.
3 Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7:203-14.