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https://www.ncbi.nlm.nih.gov/projects/Sequin/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 12,2024. Software tool for DNA sequence submission. Used for submitting and updating entries to the GenBank or EMBL sequence databases.

Proper citation: Sequin (RRID:SCR_016581) Copy   

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http://compbio.cs.princeton.edu/conservation/

Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands.

Proper citation: Conservation (RRID:SCR_016064) Copy   

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https://sites.google.com/a/blueprint.org/trades/

With Trajectory Directed Ensemble Sampling (TraDES) create large ensembles of high-quality protein structures quickly, ranging from near-native to partially unfolded to intrinsically unfolded. TraDES is a system for directly controlling and sampling protein conformational space. TraDES has been previously used for measuring the vastness of protein conformational space and testing the hypothesis of a brute force solution to the protein folding problem. Over 10 Billion protein structures have been produced by TraDES software in previous distributed computing experiments. The package is comprised of binary executable programs and accessory programs and scripts as well as protein structure data files that map out protein conformational space in a probabilistic way. The main programs are: * trades - generates protein structures following the Trajectory Distribution (see below) * seq2trj - makes Trajectory Distributions from sequences for sampling * str2tr - makes Trajectory Distributions from 3D structures for sampling Trajectory Distributions - Controlling the Sampling of Conformational Space The concept of the trajectory distribution may be new to many protein scientists. A trajectory distribution is simply a map of available conformational space at an amino acid residue. NMR scientists are the primary users of the TraDES package.

Proper citation: TraDES (RRID:SCR_006142) Copy   

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http://www.ncbi.nlm.nih.gov/igblast/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine.

Proper citation: IgBLAST (RRID:SCR_002873) Copy   

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http://www.ebi.ac.uk/Tools/blast2/index.html

It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterized genes.

Proper citation: Washington University Basic Local Alignment Search Tool (RRID:SCR_008285) Copy   

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https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/

Software tool as a command-line program that automates the creation of sequence records for submission to GenBank. Records need no additional manual editing before submission.

Proper citation: tbl2asn (RRID:SCR_016636) Copy   

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https://github.com/asdcid/Gene-conservation-informed-contig-alignment

Software tool for separation haplotigs from genome assembly. Method to separate haplotigs based on sequence similarity.

Proper citation: Gene-conservation-informed-contig-alignment (RRID:SCR_017617) Copy   

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https://github.com/liukai5016/FungiLT

Software classifier tool based on deep learning methods for classification and annotation of large-scale fungal ITS sequences. Used for fungal species classification.

Proper citation: FungiLT (RRID:SCR_025886) Copy   

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http://rgp.dna.affrc.go.jp/E/index.html

Rice Genome Research Program (RGP) is an integral part of the Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF) Genome Research Project. RGP now aims to completely sequence the entire rice genome and subsequently to pursue integrated goals in functional genomics, genome informatics and applied genomics. It is jointly coordinated by the National Institute of Agrobiological Sciences (NIAS), a government research institute under MAFF and the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), a semi-private research organization managed and supported by MAFF and a consortium of some twenty Japanese companies. The research is funded with yearly grants from MAFF and additional funds from the Japan Racing Association (JRA). It is now the leading member of the International Rice Genome Sequencing Project (IRGSP), a consortium of ten countries sharing the sequencing of the 12 rice chromosomes. The IRGSP adopts the clone-by-clone shotgun sequencing strategy so that each sequenced clone can be associated with a specific position on the genetic map and adheres to the policy of immediate release of the sequence data to the public domain. In December 2004, the IRGSP completed the sequencing of the rice genome. The high-quality and map-based sequence of the entire genome is now available in public databases.

Proper citation: Rice Genome Research Project (RRID:SCR_002268) Copy   

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http://www.ncbi.nlm.nih.gov/SNP/

Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.

Proper citation: dbSNP (RRID:SCR_002338) Copy   

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http://camera.calit2.net/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.

Proper citation: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) Copy   

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http://www.cmhd.ca/genetrap/

Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: Centre for Modeling Human Disease Gene Trap Resource (RRID:SCR_002785) Copy   

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http://www.hgsc.bcm.tmc.edu/content/honey-bee-genome-project

The HGSC has sequenced the honey bee, Apis mellifera. The version 4.0 assembly was released in March 2006 and published in October 2006. The genome sequence is being upgraded with additional sequence coverage. The honey bee is important in the agricultural community as a producer of honey and as a facilitator of pollination. It is a model organism for studying the following human health issues: immunity, allergic reaction, antibiotic resistance, development, mental health, longevity and diseases of the X chromosome. In addition, biologists are interested in the honey bee's social organization and behavioral traits. This project was proposed to the HGSC by a group of dedicated insect biologists, headed by Gene Robinson. Following a workshop at the HGSC and a honey bee white paper, the HGSC began the project in 2002. A 6-fold coverage WGS, BAC sequence from pooled arrays, and an initial genome assembly (Amel_v1.0) were released beginning in 2003. This has been a challenging project with difficulty in recovering AT-rich regions. The WGS data had lower coverage in AT-rich regions and BAC data from clones showed evidence of internal deletions. Additional reads from AT enriched DNA addressed these underrepresented regions. The current assembly Amel_4.0 was produced with Atlas and includes 2.7 million reads (1.8 Gb) or 7.5x coverage of the (clonable) genome. About 97% of STSs, 98% of ESTs, and 96% of cDNAs are represented in the 231 Mb assembly. About 2,500 reads were also produced from a strain of Africanized honey bee and SNPs were extracted. These were released in dbSNP and the NCBI Trace Archive. Analysis of the genome by a consortium of 20 labs has been completed. This produced a gene list derived from five different methods melded through the GLEAN software. Publications include a main paper in Nature and up to forty companion papers in Genome Research and Insect Molecular Biology. Sponsors: Sequencing of the honey bee is jointly funded by National Human Genome Research Institute (NHGRI) and the Department of Agriculture (USDA). Multiple drones from the same queen (strain DH4) were obtained from Danny Weaver of B. Weaver Apiaries. All libraries were made from DNA isolated from these drones. The honey bee BAC library (CHORI-224) was prepared by Pieter de Jong and Katzutoyo Osoegawa at the Children's Hospital Oakland Research Institute.

Proper citation: Honey Bee Genome Project (RRID:SCR_002890) Copy   

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http://rana.lbl.gov/drosophila

A single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing multiple_at_fruitfly.org.

Proper citation: Assembly/Alignment/Annotation of 12 Related Drosophila Species (RRID:SCR_002921) Copy   

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http://proteininformationresource.org/

Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO.

Proper citation: Protein Information Resource (RRID:SCR_002837) Copy   

•   Source: SciCrunch Registry

http://www.hgsc.bcm.tmc.edu/content/red-flour-beetle-genome-project

This portal provides information about the Tribolium castabeum Genome Project. The Tribolium castaneum genome sequence and its analysis has been published in Nature, two companion journal issues (IBMB and DGE) and numerous other publications listed below. The red flour beetle, Tribolium castaneum, a common pest that is also a genetic model for the Coleoptera. The genome has been sequenced to 7-fold coverage using a whole genome shotgun approach and assembled using the HGSC's assembly engine, Atlas, with methods employed for the Drosophila pseudoobscura genome assembly. Approximately 90% of the genome sequence has been mapped to chromosomes in collaboration with Dick Beeman (USDA ARS) and Sue Brown (Kansas State University). Access to the Data :- Genome Assembly: The long term home of the Tribolium genome is Beetlebase. Tcas 3.0 is now available in GenBank and on our FTP site. Note there are no restrictions of any kind on the Tribolium data as it has been published. Version 2 of the assembly, Tcas_2.0 is available for download using the FTP Data link in the sidebar. The assembly is described in detail in the README in that directory. T.cas_1.0 was a preliminary genome assembly that did not include large insert paired end information and has been moved to a previous assemblies folder. A genboree browser of the Tcas2.0 sequence is available here: There are also links to the genboree browser from the blast results (at the bottom of each reported HSP) if you use the blast server on this page. The original linear scaffold file, Tcas2.0/linearScaffolds/Tcas20050914-genome, posted on the ftp site did not include singleton contigs from the assembly and thus did not fully reflect the tribolium genome sequence, missing ~4.4Mb of sequence in 1860 contigs and reptigs or approximately 2.5% of the assembled sequence. A corrected Tcas20051011-genome file containing these missing sequences is now available on the ftp site. The blast databases have also been updated to reflect this change. All other data is correct, and not affected by this change. :- BLAST Searches: The BLAST link is located in the sidebar. :* Linearized chromosome and unplaced scaffold sequences :* Assembled contigs :* Bin0 unassembled reads and Repeat reads Traces are available from the NCBI Trace Archive by using the link in the sidebar, or by using NCBI MegaBLAST with a same species or cross species query. Sponsors: Funding for this project has been provided by the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH), and the U.S. Department of Agriculture's Agricultural Research Service (USDA ARS Agreement No. 58-5430-3-338).

Proper citation: Tribolium castaneum Genome Project (RRID:SCR_002848) Copy   

•   Source: SciCrunch Registry

http://hapmap.ncbi.nlm.nih.gov/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.

Proper citation: International HapMap Project (RRID:SCR_002846) Copy   

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http://hiv-web.lanl.gov/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. HIV Sequence Database is a database of annotated HIV sequences, plus a variety of tools and information for researchers studying HIV and SIV. The main aim of this website is to provide easy access to our sequence database, alignments, and the tools and interfaces we have produced. The HIV Sequence Database focuses on five primary goals: * Collecting HIV and SIV sequence data (all sequences since 1987) * Curating and annotating this data, and making it available to the scientific community * Computer analysis of HIV and related sequences * Production of software for the analysis of (sequence) data * The data and analyses on this site and published in a yearly printed publication, the HIV sequence Compendium, which is available free of charge.

Proper citation: HIV Sequence Database (RRID:SCR_002906) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/msa/clustalw2/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF.

Proper citation: Clustal W2 (RRID:SCR_002909) Copy   

•   Source: SciCrunch Registry

http://iimcb.genesilico.pl/MetaLocGramN/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice.

Proper citation: MetaLocGramN (RRID:SCR_003154) Copy   

•   Source: SciCrunch Registry