Tools   Select Another Resource Report Type

https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html

Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets.

Proper citation: BLASTClust (RRID:SCR_016641) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi

Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus.

Proper citation: Genotyping (RRID:SCR_016645) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/orffinder

Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long.

Proper citation: Open Reading Frame Finder (RRID:SCR_016643) Copy   

•   Source: SciCrunch Registry

https://picrust.github.io/picrust/

Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome.

Proper citation: PICRUSt (RRID:SCR_016855) Copy   

•   Source: SciCrunch Registry

https://github.com/TGAC/KAT

Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies.

Proper citation: KAT (RRID:SCR_016741) Copy   

•   Source: SciCrunch Registry

http://cctop.enzim.ttk.mta.hu/

Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them.

Proper citation: CCTOP (RRID:SCR_016963) Copy   

•   Source: SciCrunch Registry

http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3

Web tool to identify putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. Used for detection of known transcription regulatory elements using species-tailored searches.

Proper citation: ALGGEN-PROMO (RRID:SCR_016926) Copy   

•   Source: SciCrunch Registry

https://github.com/ToolsVanBox/smMIPfil

Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required.

Proper citation: smMIPfil (RRID:SCR_016892) Copy   

•   Source: SciCrunch Registry

http://crispr.hzau.edu.cn/CRISPR/

Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment.

Proper citation: CRISPR-P (RRID:SCR_016941) Copy   

•   Source: SciCrunch Registry

https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/

Software tool for trimming and filtering sequencing data. Used to combine data quality related trimming, filtering, and masking operations into a single tool adapter. BBDuk2 allows multiple kmer based operations in a single pass.

Proper citation: Bestus Bioinformaticus Duk (RRID:SCR_016969) Copy   

•   Source: SciCrunch Registry

https://github.com/INTABiotechMJ/MITE-Tracker

Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences.

Proper citation: MITE-Tracker (RRID:SCR_017030) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/BepiPred/index.php

Sequential B-Cell Epitope Predictor. Web server predicts B-cell epitopes from protein sequence. Sequence-based B-cell epitope prediction using conformational epitopes. Sequences of protein of interest should be in fasta format. BepiPred 2.0 is available as stand alone software package, with same functionality as web service., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BepiPred-2.0 (RRID:SCR_018499) Copy   

•   Source: SciCrunch Registry

http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html#install

Software package for sequence alignment. Pairwise aligner for aligning DNA sequences. Designed to handle sequences size of human chromosomes and from different species. Useful for sequences produced by NGS sequencing technologies.

Proper citation: LASTZ (RRID:SCR_018556) Copy   

•   Source: SciCrunch Registry

http://faculty.ucr.edu/~mmaduro/random.htm

Web application to generate random DNA sequences.

Proper citation: Random DNA Sequence Generator (RRID:SCR_018768) Copy   

•   Source: SciCrunch Registry

https://github.com/cmayer/BaitFisher-package

Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.

Proper citation: Baitfisher (RRID:SCR_015985) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/seqtools

Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments.

Proper citation: Belvu (RRID:SCR_015989) Copy   

•   Source: SciCrunch Registry

http://www.aevol.fr/

Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).

Proper citation: Aevol (RRID:SCR_015966) Copy   

•   Source: SciCrunch Registry

https://bioinf.eva.mpg.de/anfo/

Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle.

Proper citation: Anfo (RRID:SCR_015972) Copy   

•   Source: SciCrunch Registry

https://github.com/osallou/cassiopee-c

Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity.

Proper citation: Cassiopee (RRID:SCR_016056) Copy   

•   Source: SciCrunch Registry

http://cdbfasta.sourceforge.net/

Software tool for indexing and retrieval of nucleotide sequences from FASTA (DNA and protein sequence alignment software) record databases. It has the option to compress data records.

Proper citation: Cdbfasta (RRID:SCR_016057) Copy   

•   Source: SciCrunch Registry