Search Results for "c-sharp" - Page 3

A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper

SunlightCBM is a suite of perl scripts for constraint-based modelling and flux-balance analysis in metabolic networks.

This is an approach that complements previous methods for reliable homozygous structural variation identification. Our approach accurately determines genotype and breakpoints relative to a reference genome based on de novo assembly of Illumina Genome Analyzer sequencing data. In this method, we examined only homozygous structural variations because detecting heterozygous structural variations requires assembly of haplotype sequences, which is not yet possible using existing assemblers.

Gdraw is an genome visualization tool, including a GUI application and a Perl library. The GUI application creates the drawing interactively. It can also create the drawing by import annotated sequence files (such as Genbank, EMBL). Its backend library can be used in user-written perl scripts to create highly customized drawings.

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.

CisPlusFinder predicts cis-regulatory modules based on perfect local ungapped sequences using comparative sequence data from multiple organisms. An overview of the CisPlusFinder can be found in the flowchart.tif file and is described in the following publication: Pierstorff, N., C.M. Bergman & T. Wiehe. (2006) Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA. Bioinformatics 22:2858-2864. http://www.ncbi.nlm.nih.gov/pubmed/17032682

MRS is a tool to quickly and easily store and index large flat file databanks and in a space efficient manner. It is currently used to index huge bioinformatics databanks but it is not limited to this area.

The Open HeliSphere project encompasses the bioinformatics tool suite for the HeliScope single molecule sequencer.

MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.

A bioinformatics tool to identify and remove rRNA sequences from metagenomic and metatranscriptomic datasets. The rRNA-like sequences are classified by domain, subunit. and bacterial phyla. Coverage plots for the top hits are provided as well.

ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.

As an NIAID Bioinformatics Resource Center (BRC) Pathema contains in depth curatorial analysis of six target organisms from the list of NIAID category A-C pathogens. Pathema also offers single-genome and comparative multi-genome analyses as well as displ

A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.

Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.

BSmapper - Sequence mapper for bisulfite sequencing reads for DNA methylation studies. Can handle Sanger and 454 reads for mapping to whole genomes or target regions.

A set of utilities to handle individual-level genotype data files

Luminous is a set of programs and C++ classes to handle Illumina GTC files.

HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.

RAPD Primer Design from Metagenomes (RPD-M) scans metagenome sequences identifying and determining relative frequency of candidate primers for Random Amplification of Polymorphic DNA (RAPD) assays.

Common code developed by researchers in the Edwards Bioinformatics Group at SDSU. This code is free for everyone to use. It is our base code that we provide on an as-is basis. Please let us know if you use the code or have questions/comments

DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG).

Whole-genome scale multiple genome local alignment search program. Supports unlimited length gapped-seed patterns, parallelization through distributed hashing, and unique a TF-IDF based repeat filtering method.

speciateIT is a software package for speciation of 16S sequence data.

Cscape is an application for visualizing and navigating through data from a Reverse Phase Protein Microarray (RPMA). Cscape uses the Google Maps API to map the RPMA data on top of an image of a cancer cell and its associated pathways.

Biodiversity Information Group develops software tools and data standards that enable herbaria and museums to create dynamic distributed queries of their online databases. See http://bit.ly/bfirSh and http://bit.ly/bwpnSY for latest developments.