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http://cudasw.sourceforge.net/
CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher
Proper citation: CUDASW++ (RRID:SCR_008862) Copy
http://www.dnastar.com/t-sub-solutions-molecular-biology-Sanger-Sequence-Assembly.aspx
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software suite for the assembly and analysis of Sanger sequencing data within the SeqMan Pro application. The software's functions include: assembling reads into groups based on sequence names, trimming vector and poor quality data, restoration of sequence ends and designing of sequence primers.
Proper citation: DNASTAR: Lasergene Core Suite (RRID:SCR_000291) Copy
http://www.sanger.ac.uk/resources/software/vagrent/
Software tool set for calculating the biological consequences of genomic variations. The suite of perl modules compares genomic variations with reference genome annotations and generates the possible effects each variant may have on the transcripts it overlaps. It evaluates each variation/transcript combination and describes the effects in the mRNA, CDS and protein sequence contexts. It provides details of the sequence and position of the change within the transcript / protein as well as Sequence Ontology terms to classify its consequences.
Proper citation: VAGrENT (RRID:SCR_005180) Copy
https://www.ncbi.nlm.nih.gov/projects/Sequin/
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.
Proper citation: Sequin (RRID:SCR_016581) Copy
http://compbio.cs.princeton.edu/conservation/
Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands.
Proper citation: Conservation (RRID:SCR_016064) Copy
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.
Proper citation: Mash (RRID:SCR_019135) Copy
http://www.tsl.ac.uk/groups/bioinformatics/
Core develops tools for high throughput sequence data to study non reference, non model organisms.
Proper citation: Sainsbury Laboratory Bioinformatics Core Facility (RRID:SCR_017185) Copy
https://sdrc.stanford.edu/sdrc-research-cores/dgac/home/
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.
Proper citation: Stanford Diabetes Research Center Diabetes Genomics Analysis Core (RRID:SCR_016213) Copy
https://github.com/cobilab/altair
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.
Proper citation: AltaiR (RRID:SCR_024752) Copy
https://github.com/liukai5016/FungiLT
Software classifier tool based on deep learning methods for classification and annotation of large-scale fungal ITS sequences. Used for fungal species classification.
Proper citation: FungiLT (RRID:SCR_025886) Copy
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