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http://www.sanger.ac.uk/resources/software/lookseq/

A web-based application for alignment visualization, browsing and analysis of genome sequence data.

Proper citation: LookSeq (RRID:SCR_005625) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/binning/ProViDE/

A similarity based binning algorithm that uses a customized set of alignment parameter thresholds / ranges, specifically suited for the accurate taxonomic labelling of viral metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProViDE (RRID:SCR_004709) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/binning/DiScRIBinATE/

Software for accurate taxonomic classification of metagenomic sequences using a similarity based binning method. User needs to perform a similarity search of the input metagenomic sequences (reads) against the nr protein database using BLASTx search. The generated blastx output is then taken as the input by the DiScRIBinATE program.

Proper citation: DiScRIBinATE (RRID:SCR_004862) Copy   

•   Source: SciCrunch Registry

http://metaphyler.cbcb.umd.edu/

A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database.

Proper citation: MetaPhyler (RRID:SCR_004848) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/~kgaulton/chaos.shtml

A Perl-based system for annotation of variants identified in high-throughput sequencing experiments. Functionality includes annotation of variants with information relating to population genetics, known transcripts, positional records, and sequence motif-based prediction. In addition, annotated variants can be summarized and extracted to facilitate downstream analysis. There is also basic support for gene-based biological annotation, and eventually will include tools for variant and genotype analysis and visualization.

Proper citation: CHAoS (RRID:SCR_005174) Copy   

•   Source: SciCrunch Registry

http://cbrc.kaust.edu.sa/readscan/

A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets.

Proper citation: READSCAN (RRID:SCR_005204) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/

Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request.

Proper citation: Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) Copy   

•   Source: SciCrunch Registry

http://clones.invitrogen.com/cloneranger.php

The Invitrogen Clone Collection: * Ultimate ORF Clones: Full-insert sequenced human and mouse open reading frames (ORFs) in a Gateway entry vector offering the highest utility for your downstream analysis needs. * GeneStorm Clones: GeneStorm Clones are human ORFs cloned and tested for expression in a mammalian, insect, or bacterial expression system. They are sequenced for identity and classification and are not guaranteed at the nucleotide level. * Full-Length Clones: An unparalleled repository of clones enriched for full-length inserts, derived from both public and proprietary sources. * BAC/PAC Clones: Invitrogen offers several genomic libraries from a selection of tissues and sources to facilitate your research and discovery. These collections are available in a variety of formats including clones, plates, pools and high-density colony membrane filters. * Yeast Deletions: Each yeast deletion represents a unique gene-knockout of the S. cerevisiae genome. Each open reading frame is knocked out using a PCR-based gene deletion strategy. Yeast deletions are available as clones, pools, plates and complete collections. * Yeast GFP Clones: The Yeast GFP Clone Collection of S. cerevisiae tagged open reading frames were generated by Dr. Erin O''Shea and Dr. Jonathan Weissman at University of California-San Francisco. The GFP fusion proteins are integrated into the yeast chromosome through homologous recombination and are expressed using endogenous promoters.

Proper citation: Invitrogen Clones (RRID:SCR_005371) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/sites/batchentrez

Software program for loading numbers of genome records. Allows the retrieval of a large number of nucleotide sequences or protein sequences, in a batch mode, by importing a file containing a list of the desired GI or accession numbers.

Proper citation: Batch Entrez (RRID:SCR_016634) Copy   

•   Source: SciCrunch Registry

https://github.com/kblin/merge-gbk-records

Software tool to merge multiple GenBank records using defined spacer sequence.Used to turn multiple GenBank records either in multiple files or single multi-record file into single record.

Proper citation: merge-gbk-records (RRID:SCR_017968) Copy   

•   Source: SciCrunch Registry

http://www.bondxray.org/software/aline.html

Software interactive perl/tk application which can read common sequence alignment formats which the user can then alter, embellish, markup etc to produce the kind of sequence figure commonly found in biochemical articles. Extensible WYSIWYG protein sequence alignment editor for publication quality figures.

Proper citation: Aline (RRID:SCR_016886) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/SPHINX/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Hybrid binning tool that achieves high binning efficiency by utilizing both "compositional" and "similarity" features of the query sequence during the binning process. SPHINX can analyze sequences in metagenomic data sets as rapidly as composition based approaches, but nevertheless has the accuracy and specificity of similarity based algorithms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPHINX (RRID:SCR_000534) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/nast

A knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on: 1. primary sequence 2. known or predicted secondary structure 3. known or predicted tertiary contacts (optional) Additionally, NAST can use residue-resolution experimental data (e.g. hydroxyl radical footprinting) to filter the generated decoy structures. NAST uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate large numbers of plausible 3D structures that satisfy the constraints given on the secondary and tertiary structure. It then filter these structures based on agreement to the experimental data (if available). This results in a model of the molecule which satisfies all the known residue-resolution data. Imported from BiositeMaps registry

Proper citation: NAST (RRID:SCR_006995) Copy   

•   Source: SciCrunch Registry

http://sites.huji.ac.il/malaria/

Data set of metabolic pathways for the malaria parasite based on the present knowledge of parasite biochemistry and on pathways known to occur in other unicellular eukaryotes. This site extracted the pertinent information from the universal sites and presented them in an educative and informative format. The site also includes, cell-cell interactions (cytoadherence and rosetting), invasion of the erythrocyte by the parasite and transport functions. It also contains an artistic impression of the ultrastructural morphology of the interaerythrocytic cycle stages and some details about the morphology of mitochondria and the apicoplast. Most pathways are relevant to the erythrocytic phase of the parasite cycle. All maps were checked for the presence of enzyme-coding genes as they are officially annotated in the Plasmodium genome (http://plasmodb.org/). The site is constructed in a hierarchical pattern that permits logical deepening: * Grouped pathways of major chemical components or biological process ** Specific pathways or specific process *** Chemical structures of substrates and products or process **** Names of enzymes and their genes or components of process Each map is linked to other maps thus enabling to verify the origin of a substrate or the fate of a product. Clicking on the EC number that appears next to each enzyme, connects the site to BRENDA, SWISSPROT ExPASy ENZYME, PlasmoDB and to IUBMB reaction scheme. Clicking of the name of a metabolite, connects the site to KEGG thus providing its chemical structure and formula. Next to each enzyme there is a pie that depicts the stage-dependent transcription of the enzyme''s coding gene. The pie is constructed as a clock of the 48 hours of the parasite cycle, where red signifies over-transcription and green, under-transcription. Clicking on the pie links to the DeRisi/UCSF transcriptome database.

Proper citation: Malaria Parasite Metabolic Pathways (RRID:SCR_007072) Copy   

•   Source: SciCrunch Registry

http://www.chickest.udel.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A chicken EST Web site has been created to provide access to the data, and a set of unique sequences has been deposited with GenBank. This site contains over 40,000 EST sequences from the chicken cDNA libraries in the University of Delaware collection. Users can perform keyword searches, BLAST nucleotide sequences against our database, view clusters of similar or overlapping clones, and order clones. The cDNA and gene sequences of many mammalian cytokines and their receptors are known. However, corresponding information on avian cytokines is limited due to the lack of cross-species activity at the functional level or strong homology at the molecular level. To improve the efficiency of identifying cytokines and novel chicken genes, a directionally cloned cDNA library from T-cell-enriched activated chicken splenocytes was constructed, and the partial sequence of 5251 clones was obtained. Sequence clustering indicates that 2357 (42%) of the clones are present as a single copy, and 2961 are distinct clones, demonstrating the high level of complexity of this library. Comparisons of the sequence data with known DNA sequences in GenBank indicate that approximately 25% of the clones match known chicken genes, 39% have similarity to known genes in other species, and 11% had no match to any sequence in the database. Several previously uncharacterized chicken cytokines and their receptors were present in our library. This collection provides a useful database for cataloging genes expressed in T cells and a valuable resource for future investigations of gene expression in avian immunology. Therefore, the Chick EST database was created.

Proper citation: UD Chick EST Project (RRID:SCR_002236) Copy   

•   Source: SciCrunch Registry