http://bioinformatics.ca/links_directory/tag/human-genomehttp://bioinformatics.ca/links_directory/tag/human-genome/feed en http://ophid.utoronto.ca/mirDIP/mirDIP integrates twelve microRNA prediction datasets from six microRNA prediction databases, allowing users to customize their microRNA target searches.13417Tue, 21 May 2013 13:10:17 -0400 http://ophid.utoronto.ca/ophidv2.201/To faciliate experimentation and integrated computational analysis with model organism PPI networks, we have integrated known, experimental and predicted PPIs for five model organisms and human in the I2D database.13416Sun, 19 May 2013 22:50:38 -0400 http://bio-bwa.sourceforge.net/Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. 12643Wed, 22 May 2013 21:20:21 -0400 http://www.seqan.de/projects/razers.htmlRazerS allows the user to align sequencing reads of arbitrary length using either the Hamming distance or the edit distance. The tool can work either lossless or with a user-defined loss rate at higher speeds. Given the loss rate, it has an approach that guarantees not to lose more reads than specified. This enables the user to adapt to the problem at hand and provides a seamless tradeoff between sensitivity and running time. 12641Mon, 20 May 2013 08:20:14 -0400 http://i.cs.hku.hk/~ckwong3/bwtsw/BWT-SW is a local alignment tool for searching nucleotide sequences. It performs the same function as BLASTn, the BLAST program for finding regions of local similarity between nucleotide sequences. While BLAST is an approximation of the Smith-Waterman local alignment algorithm and may miss significant alignments (see BLAST Sensitivity), BWT-SW finds all local alignments.12636Tue, 21 May 2013 05:40:23 -0400 http://www.ebi.ac.uk/~zerbino/velvet/Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs. 12622Thu, 23 May 2013 03:30:47 -0400 http://www.genezilla.orgHighly reconfigurable gene finder written in C++. Graph-theoretic representations of the high scoring open reading frames are provided, allowing for exploration of sub-optimal gene models. It utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, CAP sites, and will soon model CpG islands as well. 12353Mon, 20 May 2013 15:50:36 -0400 http://gene3d.biochem.ucl.ac.uk/WebServices/The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.12180Wed, 22 May 2013 06:00:30 -0400 http://www.genenames.orggenenames.org displays all approved nomenclature within Symbol Reports that contain data curated by HUGO Gene Nomenclature Committee (HGNC) editors and links to related genomic, phenotypic and proteomic information. New features include a new Quick Gene Search, a new List Search, an integrated HGNC BioMart and a new Statistics and Downloads facility.11928Wed, 22 May 2013 06:40:22 -0400 http://www.pseudomonas.comThe Pseudomonas Genome Database integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions, experimental data, and manually curated, community-based annotation updates. Comparative genomics analyses incorporate robust genera-geared methods for predicting and clustering orthologs.11924Fri, 17 May 2013 15:30:14 -0400 http://www.sanger.ac.uk/genetics/CGP/cosmic/COSMIC curates comprehensive information on somatic mutations in human cancer. Release v48 (July 2010) describes over 136,000 coding mutations in almost 542,000 tumour samples; of the 18,490 genes documented, 4803 (26%) have one or more mutations. Full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs. Biomart allows more automated data mining and integration with other biological databases. Annotation of genomic features has become a significant focus. COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources.11912Tue, 14 May 2013 12:20:24 -0400 http://cistrome.dfci.harvard.edu/CaSNP/CaSNP database for storing and interrogating quantitative copy number alterations (CNA) data from SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, CaSNP will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study, and provide links to download the data or visualize it in UCSC Genome Browser. CaSNP also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization. 11888Wed, 22 May 2013 22:10:43 -0400 http://encodeproject.org/ENCODE/The ENCODE project has a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) serves as the central repository for ENCODE data. The DCC contains a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser. ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay.11874Wed, 22 May 2013 22:50:36 -0400 http://tiara.gmi.ac.krTotal Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). 11854Sat, 18 May 2013 08:50:43 -0400 http://www.uniprot.orgUniversal Protein Resource (UniProt) maintains a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database.11853Tue, 14 May 2013 00:50:28 -0400 https://genome-cancer.ucsc.eduThe UCSC Cancer Genomics Browser comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for multiple samples alongside their associated clinical information. Multiple data sets can be viewed simultaneously as coordinated 'heatmap tracks' to compare across studies or different data modalities. Users can order, filter, aggregate, classify and display data interactively based on any given feature set including clinical features, annotated biological pathways and user-contributed collections of genes. Integrated standard statistical tools provide dynamic quantitative analysis within all available data sets. Many new features have been added, including the hgMicroscope tumor image viewer, hgSignature for real-time genomic signature evaluation on any browser track, and 'PARADIGM' pathway tracks to display integrative pathway activities. 11838Wed, 22 May 2013 16:50:20 -0400 http://goods.ibms.sinica.edu.tw/DNVs/The duplicated gene nucleotide variants database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) promotes accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304,110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates. 11774Sat, 18 May 2013 08:40:48 -0400 http://lifecenter.sgst.cn/dbdepc/index.doA database of differentially expressed proteins in human cancers (dbDEPC) collects curated cancer proteomics data, provides a resource for information on protein-level expression changes, and explores protein profile differences among different cancers. dbDEPC currently contains 1803 proteins differentially expressed in 15 cancers, curated from 65 mass spectrometry (MS) experiments in peer-reviewed publications. 11721Thu, 23 May 2013 06:20:43 -0400 http://www.h-invitational.jp/The H-Invitational Database (H-InvDB) is a comprehensive annotation resource of human genes and transcripts. The latest release of H-InvDB (release 6.2) provides the annotation for 219,765 human transcripts in 43,159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources-'Navigation search', 'H-InvDB Enrichment Analysis Tool (HEAT)' and web service APIs.11717Wed, 22 May 2013 17:50:14 -0400 http://www.genome.ad.jp/keggThe KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular system. The KEGG DRUG database contains chemical structures and/or chemical components of all drugs in Japan, including crude drugs and TCM (Traditional Chinese Medicine) formulas, and drugs in the USA and Europe. The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets.11672Sun, 19 May 2013 21:50:35 -0400 http://satellog.bcgsc.ca/Satellog is a database for the identification and prioritization of satellite repeats in disease association studies.11443Wed, 22 May 2013 00:40:41 -0400 http://www.mutdb.org/MutDB is a database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or by various identifiers.11422Tue, 21 May 2013 21:10:23 -0400 http://bioinfo.csie.ncu.edu.tw/ProSplicer/Database which stores alternative splicing information generated from EST, mRNA and protein alignments with genomic sequence; text-based queries and graphical views of putative splice variants.11389Tue, 21 May 2013 01:50:29 -0400 http://www.hgvbaseg2p.org/indexHuman Genome Variation database - curated; attempt to summarize all known sequence variations in the human genome, to facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes.11377Mon, 20 May 2013 10:30:25 -0400 http://mgc.nci.nih.gov/Goal is to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for human and mouse; publicly accessible.11353Wed, 22 May 2013 02:20:52 -0400 http://www.ensembl.org/Mus_musculus/index.htmlAnalysis of finished and draft mouse genomic clone sequences.11352Tue, 14 May 2013 01:00:39 -0400 http://www.genecards.org/Database of human genes, their products, and involvement in diseases; free for non-commercial use, but users should also read the Terms of Use for this site.11374Sat, 18 May 2013 02:20:55 -0400 http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v35/n1s/index.htmlHands-on tutorial for using genome browsers as web tools for browsing and analyzing data from the Human Genome Project and other sequencing efforts; features UCSC Genome Browser, the NCBI Map Viewer, and the Ensembl Genome Browser.11253Wed, 22 May 2013 10:00:23 -0400 http://pir.georgetown.edu/PIR is an integrated bioinformatics resource. The Protein Sequence Database (PSD), a functionally annotated database of protein sequences, is located at PIR.11271Tue, 21 May 2013 01:40:22 -0400 http://biodas.org/This site is the center of development of an Open Source system for exchanging annotations on genomic sequence data.11186Mon, 20 May 2013 07:40:15 -0400 http://www.ensembl.org/Homo_sapiens/Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes; uses NCBI assembly.10742Thu, 23 May 2013 01:40:25 -0400 http://www.ensembl.org/Rattus_norvegicus/The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus).10741Sat, 18 May 2013 21:00:32 -0400 http://www.ensembl.org/Anopheles_gambiae/This site presents the tenfold whole genome shotgun assembly of the PEST strain of anopheles gambiae, as prepared by The International Anopheles Genome project.10740Tue, 21 May 2013 20:30:39 -0400 http://www.ensembl.org/Drosophila_melanogaster/Access to the Fly genome through the Ensembl user interface (both for visualisation and data mining).10738Thu, 23 May 2013 05:00:23 -0400 http://www.ensembl.org/Fugu_rubripes/Fugu Ensembl is a joint project between The IMCB and the EMBL - EBI to produce and maintain an automatic annotation of the Fugu Genome.10737Wed, 22 May 2013 23:40:58 -0400 http://selox.mpi-cbg.de/cgi-bin/selox/indexSeLOX web server identifies degenerate lox-like sites within genomic sequences.10712Sun, 19 May 2013 18:40:15 -0400 http://sfmap.technion.ac.ilSFmap is a web server for predicting putative splicing factor (SF) binding sites in genomic data. Sequences are input in FASTA format.10657Sun, 19 May 2013 08:40:16 -0400 http://www.lovd.nl/2.0/The Leiden Open (source) Variation Database (LOVD) To provides a flexible, freely available tool for the gene-centered collection and display of DNA variations.10621Sat, 18 May 2013 00:10:32 -0400 https://mutalyzer.nl/Mutalyzer was primarily developed to check the description of sequence variants identified in a gene during genetic testing according to the rules of the standard human sequence variant nomenclature of the Human Genome Variation Society. The Mutalyzer 2 parser is based on a formalized description of the nomenclature in Extended Backus-Naur Form. Mutalyzer applies the nomenclature rules and corrects variant descriptions accordingly.10620Wed, 22 May 2013 14:30:27 -0400 http://genepipe.ncgm.sinica.edu.tw/variowatch/main.doVarioWatch (formerly GenoWatch) is a disease gene mining browser for association study. VarioWatch annotates both known SNPs and novel variants using information from public domain websites such as NCBI, UniProt, KEGG and GO.10462Wed, 22 May 2013 03:30:41 -0400 http://bioinformoodics.jhmi.edu/quickSNP.plQuickSNP is a resource for the selection of tagSNPs in the human genome that includes a gene-centric selection module.10419Fri, 17 May 2013 10:30:15 -0400 http://indelscan.genomics.sinica.edu.tw/IndelScan/INDELSCAN is a tool for genome-wide identification of indels.10366Sun, 19 May 2013 22:10:25 -0400 http://www.ogic.ca/projects/g2d_2/G2D (Candidate Genes to Inherited Diseases) scans a human genomic region for genes related to an inherited disease. The G2D server also presents precomputed candidate genes for more than 600 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene.10347Tue, 21 May 2013 21:30:26 -0400 http://jbirc.jbic.or.jp/tact/Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project.10291Tue, 21 May 2013 03:20:16 -0400 http://bioinfo.bsd.uchicago.edu/MutScreener.htmlMutScreener is a human-specific primer design tool that considers gene annotation information to design primers for mutation screening. Users can provide custom gene annotation or use existing public gene annotations.10230Wed, 22 May 2013 21:00:17 -0400 http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.phpZinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.10224Mon, 20 May 2013 20:30:09 -0400 http://bio.math.berkeley.edu/mavid/download/MAVID performs multiple sequence alignments for large sequences, constructs phylogenetic trees and displays VISTA plots of conserved regions.10166Wed, 22 May 2013 06:50:21 -0400 http://bioapp.psych.uic.edu/DNannotator.htmDNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (<30Kb size limit).10144Fri, 17 May 2013 07:50:14 -0400 http://mulan.dcode.org/Mulan is a multiple sequence alignment tool. It employs novel algorithms such as TBA and multiTF to respectively perform alignments and discover transcription factor binding sites. Results can be viewed as dot-plots of individual sequence alignments, or dynamically browsed with the ability to zoom in from sequence conservation profiles down to the level of the individual characters of the sequence alignment.9933Mon, 20 May 2013 21:50:25 -0400 http://creme.dcode.org/CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.9892Mon, 20 May 2013 05:20:11 -0400 http://genes.mit.edu/burgelab/rescue-ese/Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes.9852Wed, 22 May 2013 18:10:20 -0400 http://www.esat.kuleuven.ac.be/~saerts/software/toucan.phpTOUCAN 2 is a regulatory sequence analysis workbench for Metazoan sequences, directly linked with the Ensembl database and implementing SOAP clients for diverse alignment and motif detection algorithms.9773Wed, 22 May 2013 12:50:34 -0400 http://bioinformatics.upmc.edu/GE2/GEDA.htmlThe Gene Expression Data Analyzer (GEDA) is a tool for discovering differential gene expression in a subset of patients. It is tailored to cancer-related microarray studies and offers extensive options for visualization, classification and normalization.9764Wed, 22 May 2013 01:30:37 -0400 http://genes.cs.wustl.edu/Twinscan is a system for predicting gene-structure in eukaryotic genomic sequences. In order to make its predictions, Twinscan combines the information from predicted coding regions and splice sites with conserservation measurements between the target sequence and sequences from a closely related genome. Currently sequences from mammalian genomes, and those of Arabidopsis thaliana, C. elegans, C. briggsae and strains JEC21 and H99 of Cryptococcus neoformans can be processed using Twinscan.9766Wed, 22 May 2013 10:10:20 -0400 http://genome.ucsc.edu/cgi-bin/hgGateway?org=SARS&db=0&hgsid=27736277Provides a rapid and reliable display of any requested portion of the SARS genome at any scale, together with dozens of aligned annotation tracks.9718Tue, 21 May 2013 04:40:16 -0400 http://lagan.stanford.edu/lagan_web/index.shtmlThe LAGAN alignment toolkit consists of components: CHAOS (a pairwise local aligner optimized for non-coding, and other poorly conserved regions of the genome.), LAGAN (a highly parametrizable pairwise global alignment program), Multi-LAGAN , and Shuffle-LAGAN (both variations of LAGAN).9705Tue, 21 May 2013 18:10:18 -0400 http://bioinformatics.bc.edu/marthlab/PolyBayesUNIX-based SNP discovery from redundant sequences; integrated with Phred/Phrap/Consed infrastructure (see DNA -- Contig Assembly); free for non-commercial use.9637Thu, 23 May 2013 00:00:33 -0400 http://rulai.cshl.org/tools/FirstEF/First Exon Finder (FirstEF) is a 5\' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree.9591Thu, 23 May 2013 01:20:47 -0400 http://www.sanger.ac.uk/resources/software/eponine/Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy.9592Wed, 22 May 2013 20:00:16 -0400 http://cbcb.umd.edu/software/GeneSplicer/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.9570Tue, 21 May 2013 21:20:33 -0400 http://genes.mit.edu/GENSCAN.htmlIdentification of complete gene structures in genomic DNA.9492Tue, 21 May 2013 21:40:24 -0400 http://www.pubgene.org/Searchable literature network of human genes with tools for gene expression analysis. Choose from the free public service, or purchase the commercial package.9478Tue, 21 May 2013 18:50:22 -0400 http://www.fugu-sg.org/Lots of information on fugu including complete draft sequence, annotations, comparative vertebrate genomics, phylogenies, publications, and information about the fugu genome project; has some very useful tools including annotation tools, an Ensembl mirror, and BLAST.9449Thu, 23 May 2013 02:20:50 -0400 http://www.phylofoot.org/consite/Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.9373Thu, 23 May 2013 02:30:46 -0400 http://ceas.cbi.pku.edu.cnCis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.9336Thu, 23 May 2013 02:10:29 -0400 http://bioinf.uni-greifswald.de/augustusAUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.9254Wed, 22 May 2013 19:40:13 -0400 http://statgen.ncsu.edu/asg/The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one or more exons and download the resulting sequence. ASG also links out to other alternative splicing databases like ProSplicer.9228Mon, 20 May 2013 08:50:10 -0400 http://bioinfo.thep.lu.se/acid.htmlThe Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ontology terms and position in the genome assembly.9215Tue, 21 May 2013 02:10:27 -0400