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http://www.csbio.sjtu.edu.cn/bioinf/euk-multi-2/

Data analysis service for predicting subcellular localization of eukaryotic proteins including those with multiple sites. Euk-mPLoc covers 22 eukaryotic subcellular locations.

Proper citation: Euk-mPLoc (RRID:SCR_011971) Copy   

•   Source: SciCrunch Registry

http://plantgrn.noble.org/psRNATarget/

A plant small RNA target analysis server which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to ?open? secondary structure around miRNA?s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript. PsRNATarget is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded miRNAs and transcript sequences; and outputs a comprehensive list of miRNA / target pairs along with the online tools for batch downloading, key word searching and results sorting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: psRNATarget (RRID:SCR_013321) Copy   

•   Source: SciCrunch Registry

http://www.homolog.us/blogs/

A blog on transcriptomics, bioinformatics and computational biology.

Proper citation: Homologus (RRID:SCR_013325) Copy   

•   Source: SciCrunch Registry

http://regrna2.mbc.nctu.edu.tw/

An integrated web server for identifying functional RNA motifs in an input RNA sequence.

Proper citation: RegRNA (RRID:SCR_013207) Copy   

•   Source: SciCrunch Registry

http://methycancer.psych.ac.cn/

Database to study interplay of DNA methylation, gene expression and cancer that hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer information from public resources, and the CpG Island (CGI) clones derived from our large-scale sequencing. Interconnections between different data types were analyzed and presented. Search tool and graphical MethyView are developed to help users access all the data and data connections and view DNA methylation in context of genomics and genetics data. The search tool and graphical MethyView are developed to help users access all the data and data connections and view DNA methylation in context of genomics and genetics data. As part of the Cancer Epigenomics Project in China, MethyCancer serves as a platform for sharing data and analytical results from the Cancer Genome/Epigenome Project in China with colleagues all over the world.

Proper citation: MethyCancer (RRID:SCR_013399) Copy   

•   Source: SciCrunch Registry

http://genes.mit.edu/GENSCAN.html

Web server for identification of complete gene structures in genomic DNA.Tool for predicting locations and exon-intron structures of genes in genomic sequences from variety of organisms. Used for prediction of complete gene structures in human genomic DNA.

Proper citation: GENSCAN (RRID:SCR_013362) Copy   

•   Source: SciCrunch Registry

http://probalign.njit.edu/probalign/login

Data analysis service that computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.

Proper citation: eProbalign (RRID:SCR_013247) Copy   

•   Source: SciCrunch Registry

http://www.antibodylink.org/

An antibody information database where antibodies are organized by the target protein UniProt id.

Proper citation: Antibody Links (RRID:SCR_013251) Copy   

•   Source: SciCrunch Registry

http://www.thegeneticgenealogist.com/

Blog that examines the intersection of traditional genealogical techniques and modern genetic research.

Proper citation: Genetic Genealogist (RRID:SCR_013102) Copy   

•   Source: SciCrunch Registry

http://www.dna.affrc.go.jp/PLACE/

A database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also contains a brief description of each motif and relevant literature with PubMed ID numbers. DDBJ/EMBL/GenBank nucleotide sequence databases accession numbers will be also included. Note: As of January 2007, PLACE is no longer updated or maintained.

Proper citation: PLACE- A Database of Plant Cis-acting Regulatory DNA Elements (RRID:SCR_013428) Copy   

•   Source: SciCrunch Registry

https://github.com/stamatak/ExaML

Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers.

Proper citation: Examl (RRID:SCR_016087) Copy   

•   Source: SciCrunch Registry

http://www.mathcs.emory.edu/panda/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Web-based software program for analyzing phosphorylation antibody arrays. It identifies phosphorylated antibodies in the microarray and statistically quantifies the extent of phosphorylation for these antibodies.

Proper citation: Phosphor Antibody Array Data Analysis (RRID:SCR_000633) Copy   

•   Source: SciCrunch Registry

http://www-personal.umich.edu/~jianghui/rseq/

A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations.

Proper citation: rSeq (RRID:SCR_000562) Copy   

•   Source: SciCrunch Registry

http://text0.mib.man.ac.uk/software/mldic/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. System that retrieves relevant UniProt IDs from BioThesaurus entries using a soft string matching algorithm.

Proper citation: Smart Dictionary Lookup (RRID:SCR_000568) Copy   

•   Source: SciCrunch Registry

http://genome.igib.res.in/tbvar/

Database of the variome of Mycobacterium tuberculosis (Mtb) comprising of over 29,000 single nucleotide variations created from re-analyzed data sets corresponding to over 400 isolates of Mtb. Using a systematic computational pipeline, potential functional variants and drug-resistance associated variants have been annotated. The database has an option to annotate variants from clinical re-sequencing of Mtb.

Proper citation: tbvar (RRID:SCR_001178) Copy   

•   Source: SciCrunch Registry

http://mirna.imbb.forth.gr/SSCprofiler.html

Tool which can be used to identify novel miRNA gene candidates in the human genome.

Proper citation: SSCprofiler (RRID:SCR_001282) Copy   

•   Source: SciCrunch Registry

http://hipipe.ncgm.sinica.edu.tw/

Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task.

Proper citation: HiPipe (RRID:SCR_001215) Copy   

•   Source: SciCrunch Registry

https://omictools.com/casvm-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented December 12, 2016. CASVM is a web server for predicting caspase cleavage sites on protein sequences based on the SVM algorithms. It can also be used for predicting non-canonical caspase substrate cleavage sites. The server has a relational database containing experimentally verified caspase substrates retrievable using accession IDs, keywords or sequence similarity.

Proper citation: CASVM (RRID:SCR_001121) Copy   

•   Source: SciCrunch Registry

https://wiki.nci.nih.gov/display/cageneindex/Cancer+Gene+Index+End+User+Documentation

THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data.

Proper citation: Cancer Gene Index (RRID:SCR_001117) Copy   

•   Source: SciCrunch Registry

http://grouthbio.com/Home_Page.html

A comprehensive listing of companies and organizations involved with genomics and molecular biology. There are lists for genome software and services, genome institutions and supplies, and general institutions.

Proper citation: Geoffs Bio-Directories (RRID:SCR_001016) Copy   

•   Source: SciCrunch Registry