Bioinformatics
Codes / Tools / Solutions Stacks
Bioconductor with R Language Environement
Bioconductor (http://www.bioconductor.org) is an open source project for the analysis and comprehension of genomic data and developed by the Fred Hutchinson Cancer Research Center and various US & international institutions. Bioconductor is based on the R programming language. There are two releases of Bioconductor every year (they appear shortly after the corresponding R release). At any one time there is a release version, which corresponds to the released version of R, and a development version, which corresponds to the development version of R. Most users will find the release version appropriate for their needs.
Blast 2.2.10
* Basic Local Alignment Search Tool
A heuristic sequence comparison algorithm that is used to search sequence databases for optimal local alignments to a query. A fast technique for detecting ungapped subsequences that match a given query sequence.
BLASTZ
BLASTZ is a multiple sequence alignment program for the whole-genome human-mouse alignments. Blastz output can be viewed with the LAJ interactive alignment viewer, converted to traditional text alignments using LAT, or you can write a program to parse it.
Blimps 3.6 SLE9
"A program to query both protein and nucleotide sequence databases with protein blocks and vice versa. The queries are single sequences or blocks. The program is available on the WWW and by e-mail server (send a message with the word "help" to find out the usage of the e-mail server) for searching multiple alignment databases with single sequences. It is available for installation on UNIX systems."
CDB Fasta SLE9
"fast indexing/retrieval of fasta records from flat file databases."
ClustalW 1.83 AltiVec version
ClustalW is a commonly-used bioinformatics application for identifying alignment within multiple DNA or protein sequences. This package is an AltiVec enabled version of ClustalW1.83 which has better performance and suitable for execution on JS20 and JS21 systems.
Elph SLE9
"ELPH is a general-purpose Gibbs sampler for finding motifs
in a set of DNA or protein sequences. The program takes as input a
set containing anywhere from a few dozen to thousands of sequences,
and searches through them for the most common motif, assuming" according to: http://www.bioinformatics.vg/newsletters/molbiolnet_newsletter_july03.htm
EMBOSS 4.0.0 on LoP
EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
Genesplicer SLE9
"A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice. It was compared to six programs representing the leading splice site detectors for Arabidopsis thaliana and Human: NetPlantGene,NetGene,HSPL,NNSplice,GENIO and SpliceView. In each case GeneSplicer performed comparably to the best alternative,in terms of both accuracy and computational efficiency."
Glimmer 2.13 SLE9
"Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach, described in our Nucleic Acids Research paper on Glimmer 1.0 and in our subsequent paper on Glimmer 2.0 , uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. Glimmer 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs.
Glimmer HMM SLE9
"GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single)." according to: http://www.genomics.jhu.edu/GlimmerHMM/
Glimmer M SLE9
"A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programing algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations. The decision about what gene model is best is a combination of the strength of the splice sites and the score of the exons generated by an interpolated Markov model (IMM). The system has been trained for Arabidopsis thaliana, Oryza sativa (rice), and Plasmodium falciparum (the malaria parasite), and should work well on closely related organisms."
Hmmer 2.3.2 IBM JS20 Suse
"Profile hidden Markov models can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.The advantage of using HMMS is that HMMS have a formal probabilistic basis and can be trained from unaligned sequences, if a trusted alignment isn't yet known. They do however make poor models of RNAs because they cannot describe base pairs. HMMER is a freely distibutable implementation of profile HMM software for protein sequence analysis. (Washington Univ.)"
HMMER v2.3.2 AltiVec Gen2 modified
HMMER v2.3.2 AltiVec Generation 2 with modification for better performance.
HMMPFAM 2.3.2 AltiVec_gen2 with reduced IO
This package is hmmpfam based on HMMER2.3.2-altivec_generation2 developed by Erik Lindahl. The improved package is designed with reduced IO overhead. Reduced IO is only implemented for serial version of hmmpfam in this package.
hmmpfam 2.3.2 with reduced IO
This package is hmmpfam based on HMMER2.3.2. The improved package is designed with reduced IO overhead. Reduced IO is only implemented for serial version of hmmpfam in this package.
Related document http://www-03.ibm.com/servers/enable/site/technical/pdfs/ec5e.pdf
Lucy 1.19 SLES9
"Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly, possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program." http://www.rcc.uga.edu/applications/bioinformatics/lucy.html
MODELTEST
MODELTEST is program for the selection the model of nucleotide substitution that best fits the data. The program chooses among 56 models, and implements three different model selection frameworks: hierarchical likelihood ratio tests (hLRTs), Akaike information criterion (AIC), and Bayesian information criterion (BIC). The program also implements the assesment of model uncertainty and tools for model averaging and calculation of parameter importance, using the AIC or the BIC.
MrBayes
MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.
Mummer 3.15
"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." http://sourceforge.net/projects/mummer/
ProbCons v1.11
PROBCONS is a novel tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracy of all alignment methods to date. The executable of this package ProbCons v1.11 is built on IBM eServer BladeCenter JS20 system running SUSE SLES9 using IBM XL C/C++ compiler version 7. The binaries are suitable for execution on systems with POWER4, POWER5 and PPC970 processors.
T-COFFEE
T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can combine sequences and structures.
Tandem (06-09-15-3)
X! tandem is an open source software that can model mass spectra with protein sequences. The executable in this package of X! tandem (tandem-linux-06-09-15-3) is built on IBM eServer BladeCenter JS20 system running SUSE SLES9 using IBM XL C/C++ compiler version 7. The binaries are suitable for execution on POWER4, POWER5 and PPC970 processors.
Tigr Assembler v2/Scan
The TIGR Assembler is the classic assembly tool developed by TIGR to build a consensus sequence from smaller sequence fragments. TIGR Assembler is comparable to Phrap and other greedy algorithm based assemblers.
