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http://perlprimer.sourceforge.net/
A free, open-source GUI software application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing.
Proper citation: PerlPrimer (RRID:SCR_012038) Copy
https://github.com/Gregor-Mendel-Institute/poolhap
Software tool for inferring haplotypes from pooled sequencing. Enables to infer strain numbers and haplotype frequencies in silico from sequences of pooled samples.
Proper citation: PoolHap (RRID:SCR_012129) Copy
Database to explore known and predicted interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. The database contains interaction information for over 68,000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database.
Proper citation: Search Tool for Interactions of Chemicals (RRID:SCR_007947) Copy
Database that provides access to mRNA sequences and associated regulatory elements that were processed from Genbank. These mRNA sequences include complete genomes, which are divided into 5-prime UTRs, 3-prime UTRs, initiation sequences, termination regions and full CDS sequences. This data can be searched for a range of properties including specific mRNA sequences, mRNA motifs, codon usage, RSCU values, information content, etc.
Proper citation: Transterm (RRID:SCR_008244) Copy
http://omicsomics.blogspot.fr/
A computational biologist''s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery.
Proper citation: OMICS! OMICS! (RRID:SCR_008533) Copy
Service that allows you to process CEL files from Affymetrix, Inc. GeneChip Exon 1.0 ST Arrays to identify alternative splicing.
Proper citation: Exon Array Analyzer (RRID:SCR_008684) Copy
We share commentaries, news and announcement that advance our goal of helping clinical labs to adopt next generation sequencing for the analysis of diagnostic gene targets.
Proper citation: Omixon blog (RRID:SCR_010020) Copy
http://mcg.ustc.edu.cn/sdap1/cpss/index.html
Computational Platform for analysis of Small RNA deep Sequencing data BioStaCs group., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CPSS (RRID:SCR_009395) Copy
http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index
Manually curated database of experimentally supported animal microRNA targets. Collection of experimentally supported miRNA gene interactions.
Proper citation: TarBase (RRID:SCR_010841) Copy
A website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis.
Proper citation: SNPs3D (RRID:SCR_010787) Copy
http://tools.genxpro.net/omiras/
A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions.
Proper citation: omiRas (RRID:SCR_010833) Copy
http://compbio.med.harvard.edu/CGHweb/
Data analysis service enabling users to analyse their array-CGH data with multiple algorithms simultaneously.
Proper citation: CGHweb (RRID:SCR_010923) Copy
http://agvgd.iarc.fr/index.php
A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral.
Proper citation: Align-GVGD (RRID:SCR_010772) Copy
http://cosmoss.org/bm/plantapdb
A phylogeny-based comprehensive database of plant transcription associated proteins.
Proper citation: PlanTAPDB (RRID:SCR_010897) Copy
http://www.mutationtaster.org/
Evaluates disease-causing potential of sequence alterations.
Proper citation: MutationTaster (RRID:SCR_010777) Copy
http://hyperbrowser.uio.no/hb/
A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets.
Proper citation: Genomic HyperBrowser (RRID:SCR_010909) Copy
https://genome-cancer.ucsc.edu/
A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets.
Proper citation: UCSC Cancer Genomics Browser (RRID:SCR_011796) Copy
http://www.ebi.ac.uk/Tools/sss/wublast/
Tool to find regions of sequence similarity within selected protein databases quickly, with minimum loss of sensitivity.
Proper citation: WU-BLAST (RRID:SCR_011824) Copy
http://data-analysis.charite.de/care/
Comprehensive database of cancer relevant proteins and compound interactions supported by experimental knowledge.Knowledgebase for drug-target relationships related to cancer as well as for supporting information or experimental data.
Proper citation: CancerResource (RRID:SCR_011945) Copy
This blog will appeal to those dealing with the practical day to day work of biological data analysis and presentation.
Proper citation: Blue Collar Bioinformatics (RRID:SCR_012913) Copy
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