RopeBWT2: Incremental construction of FM-index for DNA sequences
RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT positi...2011 days ago
BLAST options, setting and defaults
...90) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA databases. BLAST is best used...1965 days ago
genoPlotR - plot gene and genome maps project!
...format such as protein table files and blast results, as well as home-made tabular files. Features Linear representation of several segments of DNA Comparisons represented by a...1963 days ago
FGENESH - Program for predicting multiple genes in genomic DNA sequences
FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequenci...1955 days ago
IQ-TREE: Efficient software for phylogenomic inference
...ed alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100%...1895 days ago
ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
...variation on several outcomes of a ChIP-seq experiment, viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding detection, the sensitivity of inferred TF-DNA binding strength, and number...1860 days ago
HumCFS: a database of fragile sites in human chromosomes
...vidence suggests their involvement in human pathologies and they have been recognized as a preferential site for integration of exogenous oncogenic DNA viruses and hotspots for chro...1833 days ago
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1738 days ago
Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences
Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this...ment presentation styles. Miropeats enhances the utility of conventional DNA sequence comparisons when loo...1706 days ago
1565 days ago