Search Results for "binary analysis tool"

Seqs Extractor is a useful tool, and can reduce ambiguities in analyses which uses BLAST command ine, commonly in the next generation sequencing, Transcriptomics, Proteomics, etc and help extract BLASTed sequences and sequences that contains microsatellites. Seqs Extrator also turns the BLAST command line more friendly.

...MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants. MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy. ...

SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data. SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. Annotated, genome-wide SNPs and indels can also be identified if specified, and are output in human readable format. A...

ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic,...

The active use repository has migrated over to: https://github.com/darrenabbey/ymap The repository here was errantly created with some large binary files included. Attempts to extract the files from the history here have failed. A copy of the history was successfully scrubbed and then hosted at github. -------- Eukaryotic pathogens have complicated and dynamic genomes. To facilitate analysis of copy number variations (CNV), single nucleotide polymorphisms (SNPs), and loss of heterozygosity (LOH) events in Candida albicans, the most common human fungal pathogen, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains. ...

...It performs batch blast searches, so it is ideal for large multi-gene families. After collecting candidate sequences, it performs sequence alignment and deposits sequences into a fasta sequence file for downstream molecular evolutionary analysis.

FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.