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https://github.com/kblin/merge-gbk-records
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.
Proper citation: merge-gbk-records (RRID:SCR_017968) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists.
Proper citation: VectorFriends (RRID:SCR_001230) Copy
http://mouse.perlegen.com/mouse/index.html
THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Data, grouped by chromosome, available as flat files for download, of identified DNA polymorphisms (SNPs) in 15 commonly used strains of inbred laboratory mice. Perlegen's SNP, genotype (empirical and imputed), haplotype, trace, and PCR primer data has been compiled with NCBI Mouse Build information to produce data files for public use. Using high-density oligonuclueotide array technology, the study identified over 8 million SNPs and other genetic differences between these strains and the previously sequenced C57BL/6J reference strains (Phase 1). By leveraging data provided by Mark Daly's research team at the Broad Institute, genotypes were also predicted for 40 other common strains (Phase 2). Under an extension to the contract, Eleazar Eskin's group at UCLA has used this data to evaluate SNP associations with phenotypes from the Mouse Phenome Project (the Mouse Phenome Database), and to construct haplotype maps for a total of 94 inbred strains (the Mouse HapMap Project). SNP and genotype positions have been mapped from their original reference coordinates to NCBI Mouse Build 37 coordinates. Note that C57BL6/J strain was not selected for re-sequencing as this data would have been almost entirely redundant with the NCBI reference sequence. Since we did not actually determine genotypes for C57BL6/J, we did not submit genotypes for this strain to dbSNP. However, implicit genotypes for C57BL6/J can be obtained from the reference sequence at each SNP position (the reference allele is the first allele in the ALLELES column). The data is available for download in two different compressed file formats. The files are saved as both PC .zip files and Unix compressed .gz files. At this website, you can: * Learn more about the goals of the Perlegen mouse resequencing project. * Learn more about the array-based resequencing technology used in the project. * Download the SNPs, genotypes, and other data generated by the project, plus sequences of the long-range PCR primers used for SNP discovery. * Browse the mouse genome for SNPs. * View the haplotype blocks within the mouse genome. Mouse Genome Browser The Mouse Genome Browser can be used to visualize genes and the SNPs discovered in this study of genome-wide DNA variation in 15 commonly used, genetically diverse strains of inbred laboratory mice. The reference genome is the C57BL/6J strain NCBI build 37 mouse sequence. In addition to the experimentally-derived genotypes for the original 15 strains, the imputed genotypes for 40 additional inbred mouse strains can also be accessed. Mouse Haplotype Analysis The sequences of 16 commonly used, genetically diverse strains of inbred laboratory mice were analyzed to determine their haplotype structure. The Ancestry Browser shows which ancestral sequence each inbred strain most resembles, along with statistics on the pairwise similarity between the ancestral strains. The Haplotype Viewer shows the haplotype block boundaries and the pairwise similarity for all 56 strains: the 15 used for SNP discovery, the reference strain (C57BL/6J), and the 40 additional strains for which the genotypes were imputed.
Proper citation: Perlegen/NIEHS National Toxicology: Mouse Genome Resequencing Project (RRID:SCR_000726) Copy
https://www.ncbi.nlm.nih.gov/sites/batchentrez
Software program for loading numbers of genome records. Allows the retrieval of a large number of nucleotide sequences or protein sequences, in a batch mode, by importing a file containing a list of the desired GI or accession numbers.
Proper citation: Batch Entrez (RRID:SCR_016634) Copy
http://www.bondxray.org/software/aline.html
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.
Proper citation: Aline (RRID:SCR_016886) 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
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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