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http://mocklerlab.org/tools/1

An application for discovering potential splice junctions in high throughput sequencing (HTS) data.

Proper citation: Supersplat (RRID:SCR_009826) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapsnp.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software providng a method based on Bayes? theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPsnp (RRID:SCR_010602) Copy   

•   Source: SciCrunch Registry

http://www.isical.ac.in/~bioinfo_miu/targetminer20.htm

A robust tool for microRNA target prediction with systematic identification of negative examples.

Proper citation: TargetMiner (RRID:SCR_010573) Copy   

•   Source: SciCrunch Registry

http://jr-assembler.iis.sinica.edu.tw/

An assembler for the de novo assembly of large genomes using short sequence reads via jumping extension and read remapping.

Proper citation: JR-Assembler (RRID:SCR_010681) Copy   

•   Source: SciCrunch Registry

http://cseweb.ucsd.edu/~ppevzner/software.html#EULER-short

Assembly package that contains a suite of software programs for correcting errors in short reads and assembling them. The assembler may take as input classical Sanger reads, 454 sequences, and Illumina reads.

Proper citation: EULER-SR (RRID:SCR_010485) Copy   

•   Source: SciCrunch Registry

http://www.genome.duke.edu/labs/ohler/research/MUMMIE/mir.html

Software for a specific model, implemented within the MUMMIE framework, for predicting micro-RNA binding sites using PAR-CLIP data.

Proper citation: MicroMUMMIE (RRID:SCR_010847) Copy   

•   Source: SciCrunch Registry

http://mirdb.org/miRDB/

An online database for miRNA target prediction and functional annotations.

Proper citation: miRDB (RRID:SCR_010848) Copy   

•   Source: SciCrunch Registry

http://home.gwu.edu/~wpeng/Software.htm

A clustering software package for identification of enriched domains from histone modification ChIP-Seq data.

Proper citation: SICER (RRID:SCR_010843) Copy   

•   Source: SciCrunch Registry

http://www.netlab.uky.edu/p/bioinfo/MapSplice

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery.

Proper citation: MapSplice (RRID:SCR_010844) Copy   

•   Source: SciCrunch Registry

http://targetscan.org/

Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals.

Proper citation: TargetScan (RRID:SCR_010845) Copy   

•   Source: SciCrunch Registry

http://groups.csail.mit.edu/pag/mirnaminer/

A web-based tool used for homologous miRNA gene search in several species. The code is available on request.

Proper citation: miRNAminer (RRID:SCR_010850) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/mira-assembler/wiki/Home/

Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.

Proper citation: MIRA (RRID:SCR_010731) Copy   

•   Source: SciCrunch Registry

http://www.comp.nus.edu.sg/~bioinfo/peasm/PE_manual.htm

Software providing a method that eschews the traditional graph-based approach in favor of a simple 3'' extension approach that has potential to be massively parallelized.

Proper citation: PE-Assembler (RRID:SCR_010732) Copy   

•   Source: SciCrunch Registry

http://mocklerlab.org/tools/2

A quality-value guided de novo short read assembler.

Proper citation: QSRA (RRID:SCR_010733) Copy   

•   Source: SciCrunch Registry

http://compbio.med.harvard.edu/Supplements/BMCBioinfo10-2.html

Designed to identify CNVs between two genomes.

Proper citation: rSW-seq (RRID:SCR_010825) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/software/cprg/?q=node/39

An algorithm to identify chromosomal breakpoints using massively parallel next generation sequence data.

Proper citation: SegSeq (RRID:SCR_010826) 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://sapred.cbi.pku.edu.cn/

Offers the researchers an automatic pipeline to predict the disease-association of SAPs.

Proper citation: SAPRED (RRID:SCR_010785) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/services/snap/

A method for evaluating effects of single amino acid substitutions on protein function.

Proper citation: SNAP - Effects of Single Amino Acid Substitutions on Protein Function (RRID:SCR_010786) Copy   

•   Source: SciCrunch Registry

http://bg.upf.edu/transfic/home

A method to transform Functional Impact scores taking into account the differences in basal tolerance to germline SNVs of genes that belong to different functional classes.

Proper citation: TransFIC (RRID:SCR_010788) Copy   

•   Source: SciCrunch Registry