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» Boosting Relational Sequence Alignments
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IPPS
2002
IEEE
14 years 9 days ago
Aligning Two Fragmented Sequences
Upon completion of the human and mouse genome sequences, world-wide sequencing capacity will turn to other complex organisms. Current strategies call for many of these genomes to ...
Vamsi Veeramachaneni, Piotr Berman, Webb Miller
BMCBI
2010
177views more  BMCBI 2010»
13 years 7 months ago
Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets
Background: Phylogenetic analysis can be used to divide a protein family into subfamilies in the absence of experimental information. Most phylogenetic analysis methods utilize mu...
Aydin Albayrak, Hasan H. Otu, Ugur O. Sezerman
BMCBI
2007
112views more  BMCBI 2007»
13 years 7 months ago
PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments
Background: By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to ...
Daniel R. Caffrey, Paul H. Dana, Vidhya Mathur, Ma...
RECOMB
2003
Springer
14 years 7 months ago
Accurate detection of very sparse sequence motifs
Protein sequence alignments are more reliable the shorter the evolutionary distance. Here, we align distantly related proteins using many closely spaced intermediate sequences as ...
Andreas Heger, Michael Lappe, Liisa Holm
ISMB
1996
13 years 8 months ago
Parameterization Studies for the SAM and HMMER Methods of Hidden Markov Model Generation
Multiple sequence alignment of distantly related viral proteins remains a challenge to all currently available alignment methods. The hidden Markovmodel approach offers a new,flex...
Marcella A. McClure, Chris Smith, Pete Elton