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https://github.com/benedictpaten/pecan

A Java consistency based multiple sequence alignment software program.

Proper citation: Pecan (RRID:SCR_001909) 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://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://droog.gs.washington.edu/polyphred/

Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.

Proper citation: PolyPhred (RRID:SCR_002337) 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

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

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/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://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

http://mgc.nci.nih.gov/

NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).

Proper citation: Mammalian Gene Collection (RRID:SCR_007024) Copy   

•   Source: SciCrunch Registry

http://www.biorep.it/en

Offer biorepository services to public and private research institutes, to the highest standards of quality and safety with the aim of contributing to the advancement of medical research and scientific discovery. The BioRep Cell Repository establishes, maintains and distributes cell line cultures as well as DNA derived from these cultures. The scientific and business affiliation between BioRep and Coriell allows access to more than a million types of cell vials, stored in liquid nitrogen. Cells that have been stored for nearly 50 years, are still viable and available for research purposes today. Thanks to an exclusive agreement with the Coriell Institute for Medical Research, the oldest and largest biorepository of the world, BioRep is specialized in cell lines preparation, in nucleic acid extraction and long term storage in liquid nitrose (-196 degrees C) and in refrigerators (-80 degrees C) of any kind of biosamples, using procedures and standards developed by the Coriell in over 50 years of activity. BioRep and Coriell together constitute one of the few Global Biorepository able to serve the pharmaceutical industries for world wide clinical trials. BioRep facility is specifically designed to give the utmost efficiency and security by implementing Coriell procedures and standards. The BioRep Tissue Repository provides safe and secure storage of tissue specimens as required for medical research and scientific investigation. All tissues are preserved with the most current preservation techniques and processes. In addition to the storage service, BioRep provides Cell Biology, Molecular Biology, Microbiology services developed in ISO 9001:2008 certified laboratories.

Proper citation: BioRep (RRID:SCR_004907) Copy   

•   Source: SciCrunch Registry

http://www.glycosciences.de/tools/GlycoFragments/

Service that calculates and displays the main fragments (Band C-, Z- and Y-, A- and X-ions) of oligosaccharides that should occur in MS-spectra. The extended ASCII nomenclature as recommended by IUPAC is used to input the sequence of complex oligosaccharides. However, some additional input rules have to be fulfilled. In case only the topology and composition of the oligosaccharide is known, a simpler way to input carbohydrate sequences is possible. Since the hydroxyl groups of synthetic carbohydrates are often the are protected they have included a way to indicate if sugar residue are persubstituted. Please have a look at the examples of valid input structures.

Proper citation: GlycoFragment (RRID:SCR_001573) Copy   

•   Source: SciCrunch Registry