Results for "Scoring"
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..., like GEO data sets, Biomart, GO, KEGG, Atlas, ArrayExpress, and PIPAx database. As for the analytics, there is gene selection, quality control, scoring distances between experiments...3520 days ago
YASS :: genomic similarity search tool
...seeds to improve sensitivity (transition mutations are purine to purine [A<->G] or pyrimidine to pyrimidine [C<->T]) using different scoring schemes with bit-score and E-...2946 days ago
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)
...gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to loc...2706 days ago
DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes
...rs with sequence homology along with their genome coordinates. Using a scoring function which accounts for t...h DNA molecule and the BLAST E-value score between homologs, maximally scoring chains of ordered gene pairs...2655 days ago
YASRA: Reference based assembler
...eing sequenced. Mapping reads to reference genomes makes use of LASTZ (Harris et al), a pairwise sequence aligner compatible with BLASTZ. Special scoring sets were derived to improve...2643 days ago
Many-to-many pairwise alignments of two sequence sets
...optimum, by exploring all possible alignments and choosing the best. A scoring matrix is read that contains...core of an alignment is equal to the sum of the matches taken from the scoring matrix, minus penalties arisi...2168 days ago
RepeatMasker compatible blast tool
...k NCBI blastn program. These include: Support for custom matrices ( without KA-Statistics ). Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's...1997 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampl...1605 days ago
HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
...lex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid int...1452 days ago
G-NEST: The Gene NEighborhood Scoring Tool
The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin. Example data files are in the separate repository.1339 days ago
