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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ProP Server Resource Report Resource Website 50+ mentions |
ProP Server (RRID:SCR_014936) | web application, software resource | Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction. | web application, prediction, arginine, lysine, cleavage, propeptide, eukaryotic, protein, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1093/protein/gzh013 | Open source | biotools:prop, BioTools:prop | https://bio.tools/prop, https://bio.tools/prop, https://bio.tools/prop | SCR_014936 | ProP, ProP 1.0 Server, ProP 1.0 | 2026-08-06 09:28:29 | 75 | ||||||
|
Composition Profiler Resource Report Resource Website 10+ mentions |
Composition Profiler (RRID:SCR_014630) | web application, software resource | Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output. | web tool, web application, amino acid, amino acid composition, sequence, bar chart, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17578581 | Source code available, Acknowledgement requested | biotools:composition_profiler | https://bio.tools/composition_profiler | SCR_014630 | 2026-08-06 09:28:25 | 32 | |||||||
|
GeneWise Resource Report Resource Website 1000+ mentions |
GeneWise (RRID:SCR_015054) | web application, software resource | Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool. | gene alignment, dna sequence, protein sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
PMID:15123596 | Freely available, Available for download | biotools:wise | https://bio.tools/wise | SCR_015054 | 2026-08-06 09:28:28 | 1017 | |||||||
|
KMA Resource Report Resource Website 1+ mentions |
KMA (RRID:SCR_024054) | software resource, alignment software, image analysis software, data processing software, software application | Software mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.Used for aligning high quality reads against highly redundant databases, where unique matches often does not exist. Works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, based on users demands. | aligning high quality reads against highly redundant databases, aligning high quality reads, highly redundant databases, | is listed by: Debian | PMID:30157759 | Free, Available for download, Freely available, | OMICS_31606 | https://sources.debian.org/src/kma/ | SCR_024054 | kma | 2026-08-06 09:30:15 | 1 | ||||||
|
shiny-server Resource Report Resource Website 1+ mentions |
shiny-server (RRID:SCR_024334) | web application, software resource | Open Source platform to host multiple Shiny applications on single server. | multiple Shiny applications on single server, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/shiny-server/ | SCR_024334 | 2026-08-06 09:30:18 | 3 | |||||||||
|
PLAST Resource Report Resource Website |
PLAST (RRID:SCR_024170) | data analysis software, software application, software resource, data processing software | Software parallel local alignment search tool for database comparison. NGS sequence similarity search tool providing significant accelerations of seeds based heuristic comparison methods. | alignment search, database comparison, NGS sequence similarity search, | is listed by: Debian | DOI:10.1186/1471-2105-10-329 | Free, Available for download, Freely available, | OMICS_06498 | https://sources.debian.org/src/plast/ | SCR_024170 | , parallel local alignment search tool, plast | 2026-08-06 09:30:16 | 0 | ||||||
|
JAligner Resource Report Resource Website |
JAligner (RRID:SCR_024050) | software resource, alignment software, image analysis software, data processing software, software application | Open source software Java implementation of the Needleman�Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model. | Java, pairwise sequence alignment, affine gap penalty model, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20021 | https://sources.debian.org/src/jaligner/ | SCR_024050 | jaligner | 2026-08-06 09:30:14 | 0 | |||||||
|
Lambda Resource Report Resource Website 1+ mentions |
Lambda (RRID:SCR_024052) | software resource, alignment software, image analysis software, data processing software, software application | Software tool as local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools. | sequences, searches in protein, | is listed by: Debian | PMID:25161219 | Free, Available for download, Freely available, | OMICS_08009 | https://sources.debian.org/src/lambda-align/, https://github.com/seqan/lambda | SCR_024052 | Lambda: the Local Aligner for Massive Biological DatA, lambda-align, LAMBDA | 2026-08-06 09:30:18 | 1 | ||||||
|
crb-blast Resource Report Resource Website |
crb-blast (RRID:SCR_024325) | data analysis software, software application, software resource, data processing software | Software tool for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation. | finding orthologs between one set of sequences and another, genome and transcriptome annotation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/ruby-crb-blast/ | SCR_024325 | Conditional Reciprocal Best Blast | 2026-08-06 09:30:18 | 0 | ||||||||
|
spaced Resource Report Resource Website |
spaced (RRID:SCR_024345) | software resource, alignment software, image analysis software, data processing software, software application | Software for alignment free sequence comparison. Uses pattern of care and don't care positions. Compares frequencies of spaced words according to pre-defined pattern. | Compares frequencies of spaced words, according to pre-defined pattern, alignment, free sequence comparison | is listed by: Debian | PMID:25685176 | Free, Available for download, Freely available, | OMICS_05427 | https://sources.debian.org/src/spaced/ | SCR_024345 | 2026-08-06 09:30:21 | 0 | |||||||
|
Logol Resource Report Resource Website |
Logol (RRID:SCR_024104) | portal, software toolkit, data or information resource, software resource | Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic. | Pattern matching, search pattern in sequence, nucleic sequence, protein sequence, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20118 | https://sources.debian.org/src/logol/ | SCR_024104 | logol | 2026-08-06 09:30:15 | 0 | |||||||
|
purple Resource Report Resource Website |
purple (RRID:SCR_024183) | data analysis software, software application, software resource, data processing software | Software tool for selecting target specific peptide candidates directly from given proteome sequence data. | selecting target specific peptide candidates, proteome sequence data, | is listed by: Debian | PMID:31181768 | Free, Available for download, Freely available, | https://sources.debian.org/src/purple/ | SCR_024183 | Picking Unique Relevant Peptides for viraL Experiments | 2026-08-06 09:30:17 | 0 | |||||||
|
sibelia Resource Report Resource Website 1+ mentions |
sibelia (RRID:SCR_024336) | data analysis software, software application, software resource, data processing software | Software comparative genomics tool to assist biologists in analysing genomic variations that correlate with pathogens, or genomic changes that help microorganisms adapt in different environments. Used for evolutionary and genome rearrangement studies for multiple strains of microorganisms. | comparative genomics, analysing genomic variations, | is listed by: Debian | DOI:10.1007/978-3-642-40453-5_17 | Free, Available for download, Freely available, | OMICS_11719 | https://sources.debian.org/src/sibelia/ | SCR_024336 | 2026-08-06 09:30:18 | 2 | |||||||
|
sibsim4 Resource Report Resource Website |
sibsim4 (RRID:SCR_024338) | software resource, alignment software, image analysis software, data processing software, software application | Software tool designed to align expressed DNA sequence with genomic sequence, allowing for introns. | align expressed DNA sequence with genomic sequence, allowing for introns, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21290 | https://sources.debian.org/src/sibsim4/ | SCR_024338 | 2026-08-06 09:30:18 | 0 | ||||||||
|
GramAlign Resource Report Resource Website 1+ mentions |
GramAlign (RRID:SCR_024032) | software resource, alignment software, image analysis software, data processing software, software application | Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences. | Multiple Sequence Alignment, progressive Multiple Sequence Alignment, sequence distance estimation, nucleotide and amino acid sequences, | is listed by: Debian | Free, Freely available | OMICS_05314 | https://sources.debian.org/src/gramalign/ | SCR_024032 | gramalign | 2026-08-06 09:30:18 | 4 | |||||||
|
IDeFIX Resource Report Resource Website |
IDeFIX (RRID:SCR_024033) | data analysis software, software application, software resource, data processing software | Software tool for demultiplexing Illumina NGS data. Reports inconsistencies between the raw data and the Sample Sheet, checks for duplicates of indices/ index combinations in the latter and removes unwanted characters from it. Creates an IDeFIX_Report.csv containing the indices/ index combinations from the raw data and their abundance as well as their count in the Sample Sheet and the corresponding Index ID(s). | demultiplexing Illumina NGS data, reports inconsistencies, checks for duplicates of indices, removes unwanted characters, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/idefix/ | SCR_024033 | idefix | 2026-08-06 09:30:14 | 0 | ||||||||
|
GraphMap2 Resource Report Resource Website 10+ mentions |
GraphMap2 (RRID:SCR_024035) | data analysis software, software application, software resource, data processing software | Software tool as splice aware RNA-seq mapper for long reads produced by Pacific Biosciences and Oxford Nanopore devices | splice aware RNA-seq mapper, long reads, Pacific Biosciences, Oxford Nanopore, | is listed by: Debian | PMID:27079541 | Free, Available for download, Freely available, | https://sources.debian.org/src/graphmap2/ | SCR_024035 | graphmap2 | 2026-08-06 09:30:18 | 21 | |||||||
|
PCMA Resource Report Resource Website |
PCMA (RRID:SCR_024156) | software resource, alignment software, image analysis software, data processing software, software application | Software tool for multiple sequence alignment based on profile consistency. Used to construct multiple sequence alignment given set of protein sequences. | multiple sequence alignment, profile consistency, construct multiple sequence alignment, protein sequences, | is listed by: Debian | PMID:12584134 | Free, Available for download, Freely available, | OMICS_14997 | https://sources.debian.org/src/pcma/ | SCR_024156 | pcma, Profile Consistency Multiple Sequence Alignment | 2026-08-06 09:30:20 | 0 | ||||||
|
PartitionFinder Resource Report Resource Website 500+ mentions |
PartitionFinder (RRID:SCR_024157) | data analysis software, software application, software resource, data processing software | Software Python program to discover optimal partitioning schemes for DNA sequences.Used for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data. | discover optimal partitioning schemes, DNA sequences, simultaneously choosing partitioning schemes and models, phylogenetic analyses of DNA, phylogenetic analyses of protein, phylogenetic analyses of morphological data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/partitionfinder/ | SCR_024157 | partitionfinder, PartitionFinder 2 | 2026-08-06 09:30:16 | 704 | ||||||||
|
BioMAJ Resource Report Resource Website |
BioMAJ (RRID:SCR_023983) | software application, software resource, workflow software, data processing software | Software workflow engine dedicated to data synchronization and processing. Software automates the update cycle and the supervision of the locally mirrored databank repository. | workflow engine, data synchronization and processing, | is listed by: Debian | Free, Available for download, Freely available | OMICS_21717 | https://sources.debian.org/src/biomaj3/, http://genouest.github.io/biomaj/ | SCR_023983 | BioMAJ3, BIOlogie Mise A Jour, biomaj3 | 2026-08-06 09:30:14 | 0 |
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