CottonGen offers BLAST with genome, transcriptome, peptide and marker sequence databases from Gossypium species. This can be done using nucleotide sequences or peptide sequences. BLAST functionality is similar to that on NCBI. BLAST Programs:

blastn: Search a nucleotide database using a nucleotide query. blastx: Search protein database using a translated nucleotide query. tblastn: Search translated nucleotide database using a protein query.

blastp: Search protein database using a protein query. Resources in this dataset:Resource Title: Website Pointer for CottonGen BLAST Search. File Name: Web Page, url: https://www.cottongen.org/blast CottonGen offers BLAST with genome, transcriptome, peptide and marker sequence databases from Gossypium species. This can be done using nucleotide sequences or peptide sequences. BLAST functionality is similar to that on NCBI. Enter or upload FASTA sequence(s) to query and select BLAST database.

BLAST Programs:

blastn: Search a nucleotide database using a nucleotide query. blastx: Search protein database using a translated nucleotide query. tblastn: Search translated nucleotide database using a protein query. blastp: Search protein database using a protein query.

This dataset tracks the updates made on the dataset "FASTA BLAST Databases" as a repository for previous versions of the data and metadata.

This includes the December 2023 release of three related tools: PaperBLAST, Curated BLAST for Genomes, and SitesBLAST. PaperBLAST links protein sequences to papers about them and to curated annotations. Curated BLAST for Genomes uses the characterized subset of PaperBLAST's database to find candidates with a function of interest within a genome. SitesBLAST links protein sequences to functional sites, such as catalytic residues or substrate-binding residues.Most of the files are gzipped:litsearch.db -- the sqlite3 database for PaperBLAST and SitesBLAST. Also see the schema.litsearch.faa -- sequences for all of the proteins mentioned in the Gene or CuratedGene tables, in fasta formatuniq.faa -- unique sequences from litsearch.faa, in fasta format. (Also see the SeqToDuplicate table.)stats -- some statistics on the PaperBLAST databasecurated.faa -- the curated subset of PaperBLAST's database, in fasta formathassites.faa -- sequences for all the proteins mentioned in the HasSites table, in fasta format.To run the tools from these downloaded databases, you need to gunzip the files and format the BLAST databases. For more information see here.References:PaperBLAST: Text Mining Papers for Information about Homologs (mSystems, 2017)Curated BLAST for Genomes (mSystems, 2020)Interactive Analysis of Functional Residues in Protein Families (mSystems, 2022)

Custom blast blast databases for refseq mitochndrial genomes and SILVA ribosomal sequences. Code used to generate these blast databses can be found on github (https://github.com/o-william-white/custom_blastdb).

Annotation of unigenes BLAST against four different databases.

Curated database of NCBI virus genomes, formatted for BLASTn

Values shown were obtained with BLASTp. SPO11, DMC1 and MND1 are meiotic specific genes.

blastn search was performed on nucleotide sequence databases (nt). At any time instance, the Past database size is the size of the database from the previous time instance. The Present database size is the database size at the present time instance. Delta is the incremental database growth from the previous time instance to the current time instance. NCBI BLAST must be performed on the entire Present database size, while iBLAST only needs to be performed on Delta.

The goals of Antibiotic Resistance Genes Database (ARGB) are to provide a centralized compendium of information on antibiotic resistance, to facilitate the consistent annotation of resistance information in newly sequenced organisms, and also to facilitate the identification and characterization of new genes. ARGB contains six types of database groups: - Resistance Type: This database contains information, such as resistance profile, mechanism, requirement, epidemiology for each type. - Resistance Gene: This database contains information, such as resistance profile, resistance type, requirement, protein and DNA sequence for each gene.This database only includes NON-REDUNDANT, NON-VECTOR, COMPLETE genes. - Antibiotic: This database contains information, such as producer, action mechanism, resistance type, for each gene. - Resistance Gene(NonRD): This database contains the same information as Resistance Gene. It does NOT include NON-REDUNDANT, NON-VECTOR genes, but includes INCOMPLETE genes. - Resistance Gene(ALL): This database contains the same information as Resistance Gene. It includes all REDUNDANT, VECTOR AND INCOMPLETE genes. - Resistance Species: This database contains resistance profile and corresponding resistance genes for each species. Furthermore, ARDB also contians three types BLAST database: - Resistance Genes Complete: Contains only NON-REDUNDANT, NON-VECTOR, COMPLETE genes sequences. - Resistance Genes Non-redundant: Contains NON-REDUNDANT, NON-VECTOR, COMPLETE, INCOMPLETE genes sequences. - Resistance Genes All: Contains all REDUNDANT, VECTOR, COMPLETE, INCOMPLETE genes sequences. Lastly, ARDB provides four types of Analytical tools: - Normal BLAST: This function allows an user to input a DNA or protein sequence, and find similar DNA (Nucleotide BLAST) or protein (Protein BLAST) sequences using blastn, blastp, blastx, tblastn, tblastx - RPS BLAST: A web RPSBLAST (RPS BLAST) interface is provided to align a query sequence against the Position Specific Scoring Matrix (PSSM) for each type. Normally, this will give the same annotation information as using regular BLAST mentioned above. - Multiple Sequences BLAST (Genome Annotation): This function allows an user to annotate multiple (less than 5000) query sequences in FASTA format. - Mutation Resistance Identification: This function allows an user to identify mutations that will cause potential antibiotic resistance, for 12 genes (16S rRNA, 23S rRNA, gyrA, gyrB, parC, parE, rpoB, katG, pncA, embB, folP, dfr). ������ :Sponsors: ARDB is funded by Uniformed Services University of the Health Sciences, administered by the Henry Jackson Foundation. :

A BLAST database generated by downloading the NCBI's core nt database on 04/28/2025, extracting all the vertebrata sequences using the taxon id 7742, and then building a new BLAST database from the vertebrata sequences.

Source code and data files for PaperBLAST, SitesBLAST, and Curated BLAST for Genomes. The database is as of April 2022. The code is as of June 2022.

Exploding the code tarball will create a PaperBLAST/ directory. The code is in the cgi/ bin/ and lib/ subdirectories.

To install the data, create a data subdirectory, and explode the PaperBLAST_Apr2022 tarball into that directory. This includes the SQLite database (litsearch.db), and two BLAST databases (uniq.faa for PaperBLAST and hassites.faa for SitesBLAST).

For up to date code and databases, see https://github.com/morgannprice/PaperBLAST

The GenBank non-redundant protein sequence database (NRDB) is a component of the NCBI BLAST databases and contains entries from GenPept, Swissprot, PIR, PDF, PDB and NCBI RefSeq.

Sequences used as Blast database.

The CottonGen CottonCyc Pathways Database, part of CottonGen, supports searching and browsing the following CottonCyc databases:

Cyc pathways for JGI v2.0 G. raimondii D5 genome assembly

This Cyc database was constructed using PathwayTools version 20.0 using the gene models from the JGI v2.0 D5 genome assembly of Gossypium raimondii. There has been no manual curation of this Cyc database. Pathway predictions were made using PathwayTools and in-silico v2.1 annotations as provided by JGI.

Cyc pathways for CGP-BGI v1.0 G. hirsutum AD1 genome assembly

This Cyc database was constructed using PathwayTools version 20.0 using the gene models from the CGP-BGI v1.0 AD1 genome assembly of Gossypium hirsutum. There has been no manual curation of this Cyc database. Pathway predictions were made using PathwayTools and in-silico v1.0 annotations as provided by CGP-BGI. Search parameters include genes, proteins, RNAs, compounds, reactions, pathways, growth media, and BLAST search. Resources in this dataset:Resource Title: Website Pointer to CottonGen CottonCyc Pathways Database. File Name: Web Page, url: http://ptools.cottongen.org/

Blast hits of the Lymnaea TSA to different protein databases.

CottonGen (https://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data to enable basic, translational and applied research in cotton. Built using the open-source Tripal database infrastructure, CottonGen supersedes CottonDB and the Cotton Marker Database, which includes sequences, genetic and physical maps, genotypic and phenotypic markers and polymorphisms, quantitative trait loci (QTLs), pathogens, germplasm collections and trait evaluations, pedigrees, and relevant bibliographic citations, with enhanced tools for easier data sharing, mining, visualization, and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST. This project is funded/supported by Cotton Incorporated, the USDA-ARS Crop Germplasm Research Unit at College Station, TX, the Southern Association of Agricultural Experiment Station Directors, Bayer CropScience, Corteva/Agriscience, Dow/Phytogen, Monsanto, Washington State University, and NRSP10. Resources in this dataset:Resource Title: Website Pointer for CottonGen. File Name: Web Page, url: https://www.cottongen.org/ Genomic, Genetic and Breeding Resources for Cotton Research Discovery and Crop Improvement organized by :

Species (Gossypium arboreum, barbadense, herbaceum, hirsutum, raimondii, others), Data (Contributors, Download, Submission, Community Projects, Archives, Cotton Trait Ontology, Nomenclatures, and links to Variety Testing Data and NCBISRA Datasets), Search options (Colleague, Genes and Transcripts, Genotype, Germplasm, Map, Markers, Publications, QTLs, Sequences, Trait Evaluation, MegaSearch), Tools (BIMS, BLAST+, CottonCyc, JBrowse, Map Viewer, Primer3, Sequence Retrieval, Synteny Viewer), International Cotton Genome Initiative (ICGI), and Help sources (User manual, FAQs).

Also provides Quick Start links for Major Species and Tools.

Gene annotation and BLAST results against seven public databases.

The databases with representaive sequences used as the blast queries when searching for plastid 16S, rbcL and psbA, and the host 18S.

Databases:

cdd_plus_hmms: CDD HMM database plus custom DNA methylase domain HMMs

methylase_hmms: custom DNA methylase domain HMMs

restriction_enzyme_hmms: custom Restriction Enzyme domain HMMs

specificity_subunit_hmms: custom Specificity Subunit domain HMMs

subtype_hmms: DNA methylase subtype HMMs from oliveira et al. https://github.com/oliveira-lab/RMS

motif_protein_blastp: protein blast database of REBASE DNA methylase genes with known motif specificity

COInr is a non-redundant, comprehensive database of COI sequences extracted from NCBI-nt and BOLD. It is not limited to a taxon, a gene region, or a taxonomic resolution. Sequences are dereplicated between databases and within taxa.

Each taxon has a unique taxonomic Identifier (taxID), fundamental to avoid ambiguous associations of homonyms and synonyms in the source database. TaxIDs form a coherent hierarchical system fully compatible with the NCBI taxIDs allowing creating their full or ranked linages.

COInr is a good starting point to create custom databases according to the users’ needs using mkCOInr scripts available at https://github.com/meglecz/mkCOInr
It is possible to select/eliminate sequences for a list of taxa, select a specific gene region, select for minimum taxonomic resolution, add new custom sequences, and format the database for BLAST, QIIME, RDP classifiers.