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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Aline Resource Report Resource Website 1+ mentions |
Aline (RRID:SCR_016886) | software application, software resource | Software interactive perl/tk application which can read common sequence alignment formats which the user can then alter, embellish, markup etc to produce the kind of sequence figure commonly found in biochemical articles. Extensible WYSIWYG protein sequence alignment editor for publication quality figures. | protein, sequence, alignment, editor, publication, quality, alter, embellish, markup, biochemistry, bioinformatics |
is related to: University of Dundee; Scotland; United Kingdom is related to: University of Western Australia; Perth; Australia |
PMID:19390156 | Free, Available for download, Freely available | SCR_016886 | 2026-09-05 06:33:02 | 2 | |||||||||
|
Sequin Resource Report Resource Website 1+ mentions |
Sequin (RRID:SCR_016581) | software application, software resource, standalone software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 12,2024. Software tool for DNA sequence submission. Used for submitting and updating entries to the GenBank or EMBL sequence databases. | DNA, sequence, submission, GeneBank, EMBL, database | has parent organization: NCBI | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016581 | 2026-09-05 06:33:02 | 3 | ||||||||||
|
Conservation Resource Report Resource Website 1000+ mentions |
Conservation (RRID:SCR_016064) | software application, software resource, software toolkit | Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands. | scoring, protein, sequence, conservation, Jensen-Shannon, divergence, predict, catalytic, site, bound, ligands, clustal, fasta, concave | is related to: Princeton University; New Jersey; USA | NIGMS GM076275; NIH P50 GM071508; NIH T32 HG003284; NSF IIS-0612231; NSF PECASE MCB-0093399 |
PMID:17519246 | Free, Available for download | SCR_016064 | Conservation-code | 2026-09-05 06:33:01 | 1606 | |||||||
|
Mash Resource Report Resource Website 50+ mentions |
Mash (RRID:SCR_019135) | data analytics software, software application, software resource | Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated. | Genome distance estimation, metagenome distance estimation, MinHash, mutation distance, sequence, sequence set |
is listed by: Debian is listed by: OMICtools |
NHGRI ; NIH |
PMID:27323842 | Free, Available for download, Freely available | OMICS_10468 | https://mash.readthedocs.io/en/latest/, https://sources.debian.org/src/mash/ | SCR_019135 | 2026-09-05 06:33:05 | 75 | ||||||
|
merge-gbk-records Resource Report Resource Website 1+ mentions |
merge-gbk-records (RRID:SCR_017968) | software application, software resource | Software tool to merge multiple GenBank records using defined spacer sequence.Used to turn multiple GenBank records either in multiple files or single multi-record file into single record. | Merge, multiple, GenBank, record, spacer, sequence, file, single | works with: GenBank | Free, Available for download, Freely available | SCR_017968 | 2026-09-05 06:33:03 | 1 | ||||||||||
|
TraDES Resource Report Resource Website 1+ mentions |
TraDES (RRID:SCR_006142) | TraDES | software application, software resource | With Trajectory Directed Ensemble Sampling (TraDES) create large ensembles of high-quality protein structures quickly, ranging from near-native to partially unfolded to intrinsically unfolded. TraDES is a system for directly controlling and sampling protein conformational space. TraDES has been previously used for measuring the vastness of protein conformational space and testing the hypothesis of a brute force solution to the protein folding problem. Over 10 Billion protein structures have been produced by TraDES software in previous distributed computing experiments. The package is comprised of binary executable programs and accessory programs and scripts as well as protein structure data files that map out protein conformational space in a probabilistic way. The main programs are: * trades - generates protein structures following the Trajectory Distribution (see below) * seq2trj - makes Trajectory Distributions from sequences for sampling * str2tr - makes Trajectory Distributions from 3D structures for sampling Trajectory Distributions - Controlling the Sampling of Conformational Space The concept of the trajectory distribution may be new to many protein scientists. A trajectory distribution is simply a map of available conformational space at an amino acid residue. NMR scientists are the primary users of the TraDES package. | protein, protein structure, structure, trajectory, sequence, protein folding | has parent organization: Christopher Hogues Research Lab at the National University of Singapore | PMID:11746699 PMID:10737933 |
Open-source | nlx_151632 | SCR_006142 | Trajectory Directed Ensemble Sampling, TraDES - Trajectory Directed Ensemble Sampling | 2026-09-05 06:32:37 | 8 | ||||||
|
AltaiR Resource Report Resource Website 1+ mentions |
AltaiR (RRID:SCR_024752) | data analysis software, data compression software, data processing software, data visualization software, software application, software resource | Software C toolkit for alignment free and spatial temporal analysis of multi-FASTA data. Used for entangling presence of multiple sequences from epidemic and pandemic events. | alignment free, spatial temporal analysis, multi-FASTA data, sequence, analysis, multiple sequences entangling presence, , FASTA format, epidemic and pandemic events, | Genomic Data Infrastructure Fundação para a Ciência e a Tecnologia; CEECINST/00026/2018 Fundação para a Ciência e a Tecnologia; European Commision 101081813 |
Free, Available for download, Freely available | SCR_024752 | 2026-09-05 06:34:40 | 2 | ||||||||||
|
Sainsbury Laboratory Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
Sainsbury Laboratory Bioinformatics Core Facility (RRID:SCR_017185) | TSL Bioinformatics | access service resource, core facility, service resource | Core develops tools for high throughput sequence data to study non reference, non model organisms. | bioinformatics, high, throughput, sequence, data, non reference, non model, organism | Open | SCR_017185 | TSL, Core Facility, The Sainsbury Laboratory, Bioinformatics | 2026-09-05 06:34:10 | 2 | |||||||||
|
Stanford Diabetes Research Center Diabetes Genomics Analysis Core Resource Report Resource Website 1+ mentions |
Stanford Diabetes Research Center Diabetes Genomics Analysis Core (RRID:SCR_016213) | GDAC, SDRC-GDAC, SDRC | access service resource, core facility, service resource | Core facility that offers library preparation and sequencing services on a variety of platforms - Illumina HiSeq 4000, MiSeq, HiSeq 2500 and PacBio Sequel - as well as bioinformatics analysis. It can sequence a variety of commercial sample preparation kits as well as custom workflows. DGAC provides access to high throughput sequencing and analysis to researchers at the Stanford Diabetes Research Center. | library, sequence, workflow, bioinformatic, gene, analysis, sequencing |
is related to: Stanford Diabetes Research Center Diabetes Immune Monitoring Core is related to: Stanford Diabetes Research Center Stanford Islet Research Core is related to: Stanford Diabetes Research Center Diabetes Clinical and Translational Core has parent organization: Stanford University; Stanford; California is organization facet of: Stanford Diabetes Research Center |
NIDDK P30 DK116074 | Available to external user | SCR_016213 | SDRC, Genomics Analysis Core, Diabetes Genomics Analysis Core | 2026-09-05 06:34:09 | 1 | |||||||
|
FungiLT Resource Report Resource Website |
FungiLT (RRID:SCR_025886) | software application, software resource, source code | Software classifier tool based on deep learning methods for classification and annotation of large-scale fungal ITS sequences. Used for fungal species classification. | fungal species classification, classifier, classification, annotation, large-scale fungal ITS sequences, fungal ITS sequences, fungal, sequence | Free, Available for download, Freely available | SCR_025886 | 2026-09-05 06:35:09 | 0 |
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