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ISMB
1998
15 years 5 months ago
A Statistical Theory of Sequence Alignment with Gaps
Astatistical theory of local alignmentalgorithms with gaps is presented. Both the linear and logarithmic phases, as well as the phase transition separating the two phases, are des...
Dirk Drasdo, Terence Hwa, Michael Lässig
BMCBI
2010
101views more  BMCBI 2010»
15 years 4 months ago
Enrichment of homologs in insignificant BLAST hits by co-complex network alignment
Background: Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection in comparative genomics, is BLAST. Usually a stri...
Like Fokkens, Sandra M. C. Botelho, Jos Boekhorst,...
BMCBI
2007
160views more  BMCBI 2007»
15 years 4 months ago
Convergent algorithms for protein structural alignment
Background: Many algorithms exist for protein structural alignment, based on internal protein coordinates or on explicit superposition of the structures. These methods are usually...
Leandro Martínez, Roberto Andreani, Jos&eac...
BMCBI
2008
103views more  BMCBI 2008»
15 years 4 months ago
TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model
Background: Protein structure analysis and comparison are major challenges in structural bioinformatics. Despite the existence of many tools and algorithms, very few of them have ...
Mallika Veeramalai, Yuzhen Ye, Adam Godzik
BMCBI
2008
149views more  BMCBI 2008»
15 years 4 months ago
Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment s
Background: Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic d...
Olivier Bastien, Eric Maréchal