Bioinformatics tools and algorithms

From Bioinformatics.ws

Jump to: navigation, search

Bioinformatics tools and algorithms

See also; biotool.net: Bioinformatics tools and algorithms | http://bioinformatics.<wbr></wbr>org - step-by-step instructions on installation and configuration of software associated with Bioinformatics/Biological sciences research

  • EMBOSS    - The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprietary systems like GCG.
  • ADF MAGE-ML - Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML).
  • AlmaKnowledgeServer - Text mining tool for genomics, proteomics platforms and drug discovery.
  • AnnHyb - Free software for working with and managing nucleotide sequences in multiple formats. Features include sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence.
  • APBioKnoppix - Knoppix based bioinformatics software tools. Bootable from CD.
  • The ARB Project - A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization. In addition to the integrated user-interface the ARB database can be accessed using Perl or C.
  • ARCiB -- Accessible Retired Computers in Biology - NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structual biology, for software packages on various platforms.
  • BioEdit - Free Windows biological sequence alignment editor.
  • Biological Concept Diagram Editor - A tool designed for efficient knowledge and data capture from electronic resources for sharing, mining and presentation purposes.
  • biOpen - Commercial Mac OS X sequence analysis and structure visualization software.
  • Darwin - An interactive tool for peptide and nucleotide sequence analysis.
  • DNA Counter - Small free Windows program to calculate nucleotides frequencies in DNA sequences.
  • DNAMAN - Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.
  • DNPTrapper - An Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
  • Expression Profiler - An open, extensible web-based collaborative platform for microarray gene expression, sequence and PPI data analysis, exposing distinct chainable components for clustering, pattern discovery, statistics, machine-learning algorithms and visualization.
  • FASTA - William Pearson's package for fast sequence comparison tools.
  • FASTA Convertor - Free Windows tool for merging multiple FASTA files into a single FASTA file.
  • Friend - An integrated multiple structure visualization and multiple sequence alignment application. Avaliable for Windows, Linux
  • GDE - An integrated linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE). Contains binaries for Linux and Mac OS X, documentation, screenshots, references, and organism specific interfaces.
  • GeneRunner - A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
  • Genespotter - Commercial Windows software for analyzing biochip image data.
  • Genome-tools Web Interface - Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format.
  • Gints - Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
  • GoCore - GoCore is an free Excel based tool for protein sequence alignment, comparisons and functional predictions in a simple, visually appealing, manner.
  • HMMER - Profiles protein sequence data using hidden Markov models of a statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.
  • INCA - INteractive Codon Analysis - Windows software that computes and charts codon and amino acid frequencies in whole genomes. Produces fully customizable scatter plots with the possibility to export graphics or text files for further analysis. Free for academic users.
  • InsilicosViewer - A free viewer for tandem mass spectrometry proteomics data. InsilicosViewer supports mass spec data in mzXML, mzData, ANDI, and TF (RAW) formats.
  • JAligner - Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
  • JSTRING - Java program for searching Tandem Repeats (TR) in a DNA sequence. It shows the results also in a graphical format.
  • KoriBlast - Commercial graphical software for Blast searches.
  • limmaGUI - A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
  • MaGe (Magnifying Genomes) - Microbial genome Annotation System - The MaGe system offers a set of graphical interfaces which allow biologist to perform relevant expert annotation of microbial genomes.
  • MARBL - MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH.
  • Mauve - Free software for constructing global alignments of multiple rearranged genomes. The visualization environment displays sequence similarity profiles and annotated sequence features.
  • MedScan - Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
  • MELTING - Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions.
  • Meta-MEME - Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
  • MIRA - A sequence assembly suite with SNP detection for "hard" projects.
  • msa.cgb.ki.se - Open source software developed by Timo Lassmann for multiple sequence alignment, including Kalign, Kalignvu and Mumsa.
  • Nano+Bio-Centre - Offers a range of free software tools for annotating an entire genome, assembling sequences, gap closing and analysis of microarrays.
  • NCBI BLAST - BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.
  • pDRAW32 - Freeware DNA cloning, analysis and visualization software.
  • Phrap/Consed - DNA sequence assembler and finishing tools from the UW Genome Center.
  • PHRED - A widely-used program for base calling DNA sequencing trace files. Source code available and free for non-commecial users.
  • PhyloSort - A Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
  • Premier Biosoft International - Developers of software for real time PCR primer design, TaqMan, molecular beacons, SYBR green, FRET, DNA microarray analysis, restriction cloning, plasmid maps, gateway cloning, protein interaction network and functional genomics.
  • RGBG Analyzer - Commercial software to analyses the red, green, blue, and gray color values of user-selected areas of images in gif, tiff, bmp, jpeg format. Windows 2000 & XP.
  • Seqtools - Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
  • Sequence Analysis - A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
  • SeWeR - An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
  • Sfold - Predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids. The web server version is free for academic use.
  • SimGene.com - A portal to Free Molecular Biology and Bioinformatics Tools.
  • Sockeye - 3D visualisation platform for Comparative Genomics visualisation.
  • STRAP - Software supports the analysis of hundreds of proteins and integrates aa sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence, and residue annotation.
  • STRING - Search for Tandem Repeats IN Genomes. Includes C source code and examples.
  • Tandem Repeats Finder - Locates and displays tandem repeats in DNA sequences.
  • WU-BLAST - The Washington University improved version of BLAST. Free for academic users.
  • XDigitize - A Linux/Unix visualization software system for evaluation of hybridisation experiments.
  •  

 

 

  • Transcription Element Search Software (TESS)    - Very helpful software for locating and displaying transcription factor binding sites within DNA sequences - from the Univ. of Penn.
  • Verbumculus Genetic Sequence Analyzer    - An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Requires Java support in browser. Also available as a downloadable program.

     

  • Advanced Genetics Wizard - Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes.
  • Bacterial Identification - Service for the identification of bacteria and fungi sequences by sequence alignment.
  • BIOBASE - The focus of the GBF project "Molecular Bioinformatics of Gene Regulation" are regulatory genomic signals and regions that govern transcriptional control based on TRANSFAC - The Transcription Factor Database. It compiles data about gene regulatory DNA sequences and protein factors binding to and acting through them.
  • BioGRID - Database of genetic and physical interactions. It contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND.
  • BioModels Database - Resource for storing, searching and retrieving published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
  • BioMolecular Engineering Research Center - Tools and methods for computational biology. Working on secondary protein structure prediction, providing reliable profiles, and developing new ways to study molecular biology through bioinformatics.
  • Biomolecular Interaction Network Database (BIND) - BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways.
  • Bioverse - Provides a framework for exploring the relationships among the molecular, genomic, proteomic, systems, and organismal worlds.
  • Canadian Bioinformatics Help Desk - We provide bioinformatics support, services, servers, and software to Canadian researchers.
  • Carnac - A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA.
  • Center for Biological Sequence Analysis - Offers more than 30 online services for DNA and protein bioinformatics analysis.
  • Center Structural Biology: Programs and Tools - User guides and worked examples for software applications in structural and molecular biology - from Yale Univ.
  • CUBIC: Columbia University Bioinformatics Center - Features PredictProtein service for sequence analysis and protein structure prediction, META for single-page interface to validated sequence analysis, PredictNLS for prediction and analysis of nuclear localization signals, EVA for evaluation of automatic protein structure prediction servers, and DSSPcont for continuous assignment of protein secondary structure.
  • Entrez Browser - Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases.
  • ERGO - Online service integrating biological data from genomics, biochemistry, genetics and high-throughput expression profiling, to achieve a comprehensive pattern-based analysis of genes and genomes.
  • FIE (5' end Information Extraction) - Gene sequence extraction of regions around the 5'-end (promoter) and/or the translation initiation site (TIS) of a gene.
  • Functional Human Gene Network - Consolidates evidence for gene-gene interactions from HPRD, BIND, Reactome, KEGG, GO, microarray co-expression and Y2H experiments. Beautiful site design.
  • Gene and Protein Synonyms DataBase - Free service for retrieving all synonyms for a given gene or protein name.
  • Gene Expression Data Analysis - Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation.
  • Genepop on the Web - Online version of the program for populational genetics.
  • Geneva Bioinformatics (GeneBio) S.A. - GeneBio provides proteomics software tools and databases including SWISS-PROT, PROSITE, SWISS-2DPAGE and Melanie. We also offer a secure version of ExPASy molecular biology web server.
  • IBM Bioinformatics Group - Tools & Content - Several genomics and proteomics tools, including multiple alignments, gene expression analysis, tandem repeat and motif discovery.
  • iHOP - Uses the network of genes and proteins as a natural way of accessing the millions of biomedical abstracts in PubMed.
  • INCBI Irish National Centre for BioInformatics - Hosts Irish embnet node, Gives links to Database browsing and interrogation at SRS, European (EBI) servers, Blast server for parasite genomes (EBI), US (NCBI) servers, Protein structure prediction, PredictProtein Server in Heidelberg, Gene identification, splice sites, exons, introns and a list of gene structure prediction programs
  • Information Génomique et Structurale (CNRS) - Online services including T-Coffee, El-Nemo, Casper and FeeBack.
  • InstaSeq - Google-based search engine for DNA, RNA or Protein sequences.
  • JustBio: Online Tool Set - A Suite of Online tools for analysis of DNA/RNA, Proteins, and Arrays.
  • Ligand-Gated Ion Channel Database - LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels.
  • LongTrace DNA Sequencing Service - A commercial service for improving the read length and quality of ABI 3730, 3130 and 3100 DNA sequencing traces. Works via reprocessing of the raw peak data before re-base calling. A free trial is provided.
  • MedMiner - An Internet biomedical data-mining tool for organizing search information gathered from textual or genetic databases - from the NIH National Cancer Inst.
  • Molecular Informatics Resource for the Analysis of Gene Expression - Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction from the Institute for Transcriptional Informatics.
  • Molecular Interactions Database (MINT) - MINT is a database designed to store functional interactions between biological molecules (proteins, RNA, DNA).
  • Mulan - Performs single-coverage local multiple DNA sequence alignments of finished and draft-quality genome sequences. It also provides with an option to predict transcription factor binding sites evolutionarily conserved across multiple species.
  • My Genomics Resource Centre - A Malaysian Genomics toolset for high-throughput analysis of biological data. Must register to use.
  • NIH BioInformatics and Molecular Analysis Section - Numerous computational tools and resources to unite advances in biology with those in computers, informatics, and networking for the genomic and genetic analysis fields of BioInformatics; division of the Computational Bioscience and Engineering Lab at the Center for Information Technology.
  • PANDORA - Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences.
  • ParAlign - Service using the ParAlign algorithm to compare genetic sequences. Apparently it is as fast as BLAST and as sensitive as Smith-Waterman.
  • PEDANT - Completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes
  • PIR-International Protein Sequence Database - produces a comprehensive, non-redundant, and expertly annotated protein sequence database. PIR features integrated annotation search to support functional/structural genomics and proteomic research.
  • PlasMapper - Online service to generate annotated plasmid maps up to 20 kbp. Outputs in PNG, JPG, SVG or SVGZ format.
  • ProCKSI: Similarity Comparison of Proteins using Contact Maps - A meta-server and decision support system for Protein Comparison, Knowledge, Similarity and Information, using protein contact maps.
  • ProPred-I - An online service for predicting MHC binding regions in antigens. It also offers the proteasomal and immunoproteasomal filters to improve the applicability of results.
  • ProteinLounge - Bioinformatics portal which integrates protein information and many databases and research tools useful for researchers and students. Subscription based service.
  • PubCrawler - An online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.
  • QGRS Mapper - Generates information on composition and distribution of putative Quadruplex forming G-Rich Sequences (QGRS) in nucleotide sequences and NCBI genes.
  • QualTrace DNA Sequencing - A free online version of the QualTrace DNA sequencing software for quality control analysis of ABI 3730 & 3730xl traces files.
  • ReadSeq - Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others.
  • SA National Bioinformatics Institute - SANBI aims to bring genome information, computational biology, and analytical tools to the South African research community. Hosts SA National EMBNet Node, provides links to Sequence Retrieval System (SRS), GeneKraal, and TB Genomes Analysis Server. Research in Sequence Tag Alignment and Consensus Knowledgebase (STACK). Databases include BLAST search in Mycobacterium genome.
  • Scansite - Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.
  • Searching GenBank - Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI).
  • Sequence Analysis (Bielefeld University Bioinformatics Server) - Collection of sequence analysis tools.
  • Simulation programs for teaching population dynamics - Offers a number of educational programs including LESLIE, LOGIST, CHAOS, CELLS, WITCOM, PRED and LEWONTIN.
  • Systems Biology of Photosynthesis - Open web platform for modeling and reverse engineering of photosynthetic dynamism.
  • TFM Explorer - Scans sequences for potential Transcription Factor binding sites using Patser and TRANSFAC.
  • Transterm - a database of mRNA regions and motifs - Transterm - an interactive database of mRNA regions and motifs from all species and genomes. Users can browse the pre-computed data tables, search the sequence databases or search their own sequences.
  • Virtual Genome Center - Online computational resources for PCR primer selection, similarity searching- from the Univ. of Minnesota.
  • Web Services at Institute of Microbial Technology, Chandigarh, India - Protein structure prediction (Protein Structural Classes, Secondary Structure Prediction), immunological methods (ProPred), genomics & proteomics (Genome Wise Sequence Similarity Search, Spectral Repeat Finder, 2D Gel Comparison, protein coding gene by Fast Fourier Transform), and biological databases.
  • WebACT - A database of sequence comparisons between all publicly available prokaryotic genome sequences, allowing the on-line visualisation of comparisons between up to five genomic sequences, using the Artemis Comparison Tool. User can perform their comparisons on their own data.
  • YMF - DNA Motif Finding Program - Finds novel transcription factor binding sites by searching for over-represented (most significant motifs) motifs in DNA sequences.
  • Zinc Finger Tools - Helps users design zinc finger transcription factors.

 

Retrieved from "http://Bioinformatics.ws/index.php/Bioinformatics_tools_and_algorithms"