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http://sift.bii.a-star.edu.sg/

Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available.

Proper citation: SIFT (RRID:SCR_012813) Copy   

•   Source: SciCrunch Registry

http://www.mrc-lmb.cam.ac.uk/genomes/dolop/

DOLOP is an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. This website along will have additional information on the biosynthetic pathway, supplementary material and other related figures. DOLOP also contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. Additionally, the website features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins.

Proper citation: DOLOP: A Database of Bacterial Lipoproteins (RRID:SCR_013487) Copy   

•   Source: SciCrunch Registry

http://research-pub.gene.com/gmap/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A software program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing.

Proper citation: GMAP (RRID:SCR_008992) Copy   

•   Source: SciCrunch Registry

https://gmod.org/wiki/CMap.1

Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software)

Proper citation: CMAP (RRID:SCR_009034) Copy   

•   Source: SciCrunch Registry

http://mafft.cbrc.jp/alignment/server/

Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.

Proper citation: MAFFT (RRID:SCR_011811) Copy   

•   Source: SciCrunch Registry

http://www.evocontology.org/site/Main/EvocOntologyDotOrg

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information.

Proper citation: eVOC (RRID:SCR_010704) Copy   

•   Source: SciCrunch Registry

https://www.mdc-berlin.de/8551903/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep

Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data.

Proper citation: miRDeep (RRID:SCR_010829) Copy   

•   Source: SciCrunch Registry

http://technelysium.com.au/?page_id=27

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Software which is able to assemble data from 454 and Illumina next-generation sequencers, with up to 100,000 sequences if 2 Gb RAM is available.

Proper citation: ChromasPro (RRID:SCR_000229) Copy   

•   Source: SciCrunch Registry

http://www.dnastar.com/t-seqmanpro.aspx

Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen.

Proper citation: Lasergene's SeqMan Pro (RRID:SCR_000283) 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

http://www.isrec.isb-sib.ch/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Computational Cancer Genomics (CCG) group is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions. Sponsors: This group is supported by the Swiss Institute of Bioinformatics (SIB).

Proper citation: Computational Cancer Genomics Group (RRID:SCR_000772) Copy   

•   Source: SciCrunch Registry

http://www.genet.sickkids.on.ca/cftr/

Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world.

Proper citation: Cystic Fibrosis Mutation Database (RRID:SCR_000685) Copy   

•   Source: SciCrunch Registry

http://megasoftware.net/

Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny.

Proper citation: MEGA (RRID:SCR_000667) Copy   

•   Source: SciCrunch Registry

http://sfld.rbvi.ucsf.edu/

A database of hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities. The SFLD classifies evolutionarily related enzymes according to shared chemical functions and maps these shared functions to conserved active site features. The classification is hierarchical, where broader levels encompass more distantly related proteins with fewer shared features. It thus serves as the analysis and archive site for superfamilies targeted by the Enzyme Function Initiative, and is developed by the Babbitt Laboratory in collaboration with the UCSF Resource for Biocomputing, Visualization, and Informatics. The resource also provides a collection of tools and data for investigating sequence-structure-function relationships and hypothesizing function.

Proper citation: Structure-function linkage database (RRID:SCR_001375) Copy   

•   Source: SciCrunch Registry

https://www.ddbj.nig.ac.jp/dra/index-e.html

Archive database for output data generated by next-generation sequencing machines including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, and others. DRA is a member of the International Nucleotide Sequence Database Collaboration (INSDC) and archiving the data in a close collaboration with NCBI Sequence Read Archive (SRA) and EBI Sequence Read Archive (ERA). Please submit the trace data from conventional capillary sequencers to DDBJ Trace Archive., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DDBJ Sequence Read Archive (RRID:SCR_001370) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/services/NetNGlyc-1.0/

Server that predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. NetNGlyc 1.0 is also available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms.

Proper citation: NetNGlyc (RRID:SCR_001570) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/services/YinOYang-1.2/

Server that produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify Yin-Yang sites. YinOYang 1.2 is available as a stand-alone software package, with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms.

Proper citation: YinOYang (RRID:SCR_001605) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/jdispatcher/msa/clustalo?stype=protein

Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.

Proper citation: Clustal Omega (RRID:SCR_001591) Copy   

•   Source: SciCrunch Registry

http://gmod.org/wiki/Main_Page

A collection of open source software tools for creating and managing genome-scale biological databases. GMOD is made up databases, applications, and adaptor software that connects these components together. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. At first GMOD just featured model organisms but now any organism with any kind of sequence associated with it is a good candidate as a subject for a GMOD database. There are GMOD databases with just protein sequence in them, with EST sequence only, those that are concerned primarily with gene expression, and even those dedicated to collections of RNA sequence. They have also heard of GMOD databases for oligonucleotides and plasmids.

Proper citation: Generic Model Organism Database Project (RRID:SCR_001731) Copy   

•   Source: SciCrunch Registry

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&BLAST_PROGRAMS=blastx&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome

Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level.

Proper citation: BLASTX (RRID:SCR_001653) Copy   

•   Source: SciCrunch Registry