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BMCBI
2005
122views more  BMCBI 2005»
13 years 5 months ago
ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequenc
Background: Currently available methods to predict splice sites are mainly based on the independent and progressive alignment of transcript data (mostly ESTs) to the genomic seque...
Paola Bonizzoni, Raffaella Rizzi, Graziano Pesole
BMCBI
2004
196views more  BMCBI 2004»
13 years 5 months ago
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Background: In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUS...
Robert C. Edgar
RECOMB
2005
Springer
14 years 5 months ago
Information Theoretic Approaches to Whole Genome Phylogenies
We describe a novel method for efficient reconstruction of phylogenetic trees, based on sequences of whole genomes or proteomes, whose lengths may greatly vary. The core of our me...
David Burstein, Igor Ulitsky, Tamir Tuller, Benny ...
ALMOB
2008
160views more  ALMOB 2008»
13 years 5 months ago
Syntenator: Multiple gene order alignments with a gene-specific scoring function
Background: Identification of homologous regions or conserved syntenies across genomes is one crucial step in comparative genomics. This task is usually performed by genome alignm...
Christian Rödelsperger, Christoph Dieterich
BMCBI
2008
121views more  BMCBI 2008»
13 years 5 months ago
ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequen
Background: Detecting conserved noncoding sequences (CNSs) across species highlights the functional elements. Alignment procedures combined with computational prediction of transc...
Hisakazu Iwama, Yukio Hori, Kensuke Matsumoto, Koj...