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http://mimirna.centenary.org.au/mireval/
A web tool for simple microRNA prediction in genome sequences.
Proper citation: miREval (RRID:SCR_010830) Copy
A collaborative project to better understand the relationship between genotype and phenotype in humans that connects human phenotype and clinical data in various locus-specific mutation databases (LSDBs) with data on genome sequences, evolutionary history, and function in the UCSC Genome Browser. PhenCode is a collaboration among researchers at Penn State, UC Santa Cruz, and locus experts at other institutions.
Proper citation: PhenCode (RRID:SCR_010799) Copy
http://159.149.160.51/pscan_chip_dev/
Web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria.
Proper citation: Pscan-ChIP (RRID:SCR_010885) Copy
http://www.unc.edu/~yunmli/1000G-imp/
A comprehensive SNP and indel imputability database.
Proper citation: SNP and indel Imputability (RRID:SCR_010800) Copy
A tool to predict changes in protein stability upon point mutations.
Proper citation: CUPSAT (RRID:SCR_010773) Copy
http://ls-snp.icm.jhu.edu/ls-snp-pdb/
A web tool for genome-wide annotation of human SNPs.
Proper citation: LS-SNP/PDB (RRID:SCR_010774) Copy
http://legumetfdb.psc.riken.jp/
A public database that provides predicted transcription factor (TF) encoding genes annotated in genome sequences of three major legume species: soybean (Glycine max), Lotus japonicus and Medicago truncatula.
Proper citation: LegumeTFDB (RRID:SCR_010896) Copy
http://bleoberis.bioc.cam.ac.uk/mcsm
Data analysis service to the study of missense mutations which relies on graph-based signatures.
Proper citation: mCSM (RRID:SCR_010776) Copy
http://plantgrn.noble.org/PlantTFcat/
A web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by systematically analyzing InterProScan domain patterns in protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PlantTFcat (RRID:SCR_010898) Copy
http://www.imgt.org/IMGT_vquest/share/textes/
Data analysis service for the standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. It identifies the variable (V), diversity (D) and joining (J) genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. New functionalities were added through a complete rewrite in Java. IMGT/V-QUEST analyses batches of sequences (up to 50) in a single run. IMGT/V-QUEST describes the V-REGION mutations and identifies the hot spot positions in the closest germline V gene. IMGT/V-QUEST can detect insertions and deletions in the submitted sequences by reference to the IMGT unique numbering. IMGT/V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions, and IMGT/Automat for a full V-J- and V-D-J-REGION annotation. IMGT/V-QUEST displays, in ''Detailed view'', the results and alignments for each submitted sequence individually and, in ''Synthesis view'', the alignments of the sequences that, in a given run, express the same V gene and allele.
Proper citation: IMGT/V-QUEST (RRID:SCR_010749) Copy
http://treetfdb.bmep.riken.jp/index.pl
A public database that provides the complete transcription factor (TF) repertoires of 6 genome sequenced tree species: papaya (Carica papaya), jatoropha (Jatropha curcas), cassava (Manihot esculenta), poplar (Populus trichocarpa), castor bean (Ricinus communis) and grape vine (Vitis vinifera). from annotated genes on each genome.
Proper citation: TreeTFDB (RRID:SCR_010901) Copy
Data analysis service providing a motif discovery platform developed to help biologists to find novel as well as known motifs in their peak datasets from transcription factor (TF) binding experiments such as ChIP-seq and ChIP-chip.
Proper citation: CompleteMOTIFs (RRID:SCR_010878) Copy
http://tcoffee.crg.cat/apps/tcoffee/do:regular
A multiple sequence alignment server which can align Protein, DNA and RNA sequences.
Proper citation: T-Coffee (RRID:SCR_011818) Copy
http://www.cbs.dtu.dk/services/HMMgene/
Data analysis service for prediction of vertebrate and C. elegans genes.
Proper citation: HMMgene (RRID:SCR_011933) Copy
Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.
Proper citation: ProbCons (RRID:SCR_011813) Copy
http://genevenn.sourceforge.net/
A web application creating Venn diagrams from two or three gene lists.
Proper citation: GeneVenn (RRID:SCR_012117) Copy
Blog where you will find a genomics resources news portal with daily postings about genomics resources, genomics news and research, science and more.
Proper citation: OpenHelix Blog (RRID:SCR_012755) Copy
A central hub of content collected from bloggers who write about R (in English).
Proper citation: R-Bloggers.com (RRID:SCR_012876) Copy
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-S1-S21
A microarray platform that uses the Illumina and Affymetrix GeneChip microarray technology for genome and transcriptome analyses and a web-based database that consists exclusively of high quality Affymetrix data from immunological experiments hosted by a public, non-profit consortium of three scientific public institutions aimed to develop, integrate and disseminate Functional Genomics.
Proper citation: Genopolis (RRID:SCR_010975) Copy
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
Tool to search translated nucleotide databases using a protein query.
Proper citation: TBLASTN (RRID:SCR_011822) Copy
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