roteinProphet(TM) automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST. Importantly, it addresses two critical issues: (1) Peptides corresponding to 'single-hit' proteins (those to which no ot...
Byne integrates ByOnic's peptide identifications into a list of proteins, ranked by confidence (p-value). The combination of ByOnic and ComByne greatly outperforms current standards, such as Mascot and ProteinProphet. ByOnic typically identifies 50 to 100 percent more spectra. On comple...
Empirical Bayes Protein identification algorithm. EBP is the first generally applicable protein identification method that can combine the results of multiple search algorithms and replicated LC MS/MS experiments. EBP is compatible with the Trans-Proteomic Pipeline (TPP) from http://sys...
This tool, of course, can not only be used for comparing methods, but also for investigating potential regulators and co-regulators of gene sets from experiments such as ChIP-chip and microarrays.
CarthaGène is a genetic/radiated hybrid mapping software. CarthaGene looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms.
ChIPDiff provides a solution for the identification of Differential Histone Modification Sites (DHMSs) by comparing two ChIP-seq libraries (L1 and L2). An HMM is employed in ChIPDiff to infer the states of histone modification changes.
DSK is a k-mer counting software, similar to Jellyfish. Jellyfish is very fast but limited to large-memory servers and k ≤ 32. In contrast, DSK supports large values of k, and runs with (almost-)arbitrarily low memory usage and reasonably low temporary disk usage. DSK can count k-mers o...
The FindPeaks application can be used for several purposes: Converting Eland, Maq (.map), BED or other files into WIG files (See Supported Input formats) ，Identifying areas of enrichment (ChIP-Seq analysis), Noise estimation in quantifying enrichment (in progress)
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libstdc++, libgcj,...). GCC was originally written as the compiler for the GNU operating system. The GNU system was developed to be 100% free so...
Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.
UCSC genome browser 'kent' bioinformatic utilities These are only the command line bioinformatic utilities from the kent source tree. This is not the genome browser install.
WebLogo 3 (http://code.google.com/p/weblogo/) is a tool for creating sequence logos from biological sequence alignments. It can be run on the command line, as a standalone webserver, as a CGI webapp, or as a python library.