Tag: sequence assembly

The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene pro ...

Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignm ...

The Dfam database is a open collection of DNA Transposable Element sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations. Dfam represents a collection of multiple sequence alignments, each containing a set of r ...

This ensembl website features the zebrafish whole genome shotgun assembly sequence.

Genome database of the beetle Tribolium castaneum

The Joint Genome Institute Genome Portal contains browseable and blastable genome assemblies for several organisms, including Pufferfish, Frog, and Sea squirt.

The JGI Genome Portal provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and in ...

The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarra ...

A database of eukaryotic sequencing projects

> CORRECT NAME OF TOOL COULD ALSO BE 'TreeshrewDB v2.0' | Chromosomal level assembly and population sequencing of the Chinese tree shrew genome | Symbol Accession number Full gene name | &nbspFan Y, Yu D et al., 2014. Tree shrew database (TreeshrewDB ...

A comprehensive resource for the genes retained from whole genome duplication in vertebrates. The code repository for OHNOLOGS v2.0 sever and multi-genome synteny comparison. A Repository of Genes Retained from Whole Genome Duplications in the Vert ...

A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.

Assembled partial genomes for ~250 eukaryotic organisms

Sciatic Nerve Atlas (SNAT) is a database med transcriptional profiling of mouse peripheral nerves to the single-cell level.

Annotated reference dataset for transcriptional start sites (TSS) in human and mouse.

Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information. The first Korean Reference Genome. KOREF_S means KOREF_Single.

The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ...

A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance. A high-quality chromosome-level genome sequence of alkaligrass assembled from Illumina, PacBio and 10× Genomics reads combined with genome-wide chromosom ...

A gene Expression Browser for RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics.

GEnetic Antibiotic Resistance and Susceptibility Database.

KAIKObase is a silkworm genome database.

Integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding.

An informational platform for genome biology of grass carp. Grass carp (Ctenopharyngodon idellus) is a herbivorous, freshwater fish species of the family Cyprinidae, and the only species of the genus Ctenopharyngodon.

SAPdb (Self Assembling Peptides Database) is a database of short peptides and the corresponding nanostructures formed by self-assembly.

The human Ensemble Cell Atlas (hECA) a database.

ViroidDB is the most comprehensive collection of viroid, satellite RNA, retrozyme, and deltavirus genome sequences available on the internet.

A database of genus characteristics of proteins and RNA. A database of genus characteristics. The Genus database collects information about topological structure and complexity of proteins and RNA chains, which is captured by the genus of a given c ...

Anti-CRISPRdb is a comprehensive online resource that effectively organizes anti-CRISPR proteins determined by experimental and bioinformatics methods. Additionally, it also provides nucleotide sequences, interactors, three-dimensional structures, ...

Global genomic population structure of Clostridioides difficile

A Grameneae Genome Alignment Database of Homologous Genes Hierarchically Related to Evolutionary Events.

A comprehensive genome platform for Brassicaceae plants.

Platform for storing and using pangenomes for imputation.

A comprehensive repetitive sequence database of over 80 000 species.

A free database of GC and many other skews for over 30,200 chromosomes and plasmids.

CoxBase is an online platform for epidemiological surveillance, visualization, analysis and typing of Coxiella burnetii genomic sequence.

An integrated transcriptomic and genomic database for Bombyx mori and related species.

The Chordata Olfactory Receptor Database (CORD) build from the annotation data from the command line tool Genome2OR

Fuzzle 2.0 is a database of evolutionary related protein fragments.

A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.

A collective database of helmeted guinea fowl genomics. Helmeted guinea fowl (HGF; Numida meleagris) is vigorous, hardy, and mostly disease-free game birds. The rearing of HGF is a potential alternative poultry system. Because of the characteristics ...

This website contains implementations of the MGT for various species. The MGT and metadata is searchable to allow identification of GTs associated with spatial, temporal or clinical characteristics.

EchinoDB is a database consisting of amino acid sequence othoclusters from 42 echinoderm transcriptomes. We sampled taxa to span the deepest divergences within each of the 5 extant echinoderm classes. Data can be searched by keywords such as annotati ...

Co-expression Network Database for <i>de novo</i> Transcriptome Assembly of <i>Paeonia lactiflora</i> Pall. Paeonia lactiflora Pall., commonly known as the herbaceous peony, is an ornamental flowering plant known around the world. Its oil contains a ...

CarrotOmics is an integrated web-based relational database, developed to house and integrate genomic, genetic and breeding data for carrot and related species. CarrotOmics includes genome assemblies, annotated transcripts, traits, maps, and markers b ...

Staphopia is a database focusing on the genomes of the bacterial pathogen Staphylococcus aureus. Life-threatening Methicillin-resistant S. aureus (MRSA) infections strike across our society, both in the community and hospital settings. In recent year ...

The Bacterial Microcompartment Database. MCPdb – The Bacterial Microcompartment Databse. MCPDB A bacterial microcompartment database and structure viewer include Carboxysome Pdu Eut BMC BMV MCP organelle encapsulin protein capsid. MCPdb is an onli ...

Simple containerised setup of a custom Ensembl database and web server for any species. Forked from molluscdb/molluscdb-plugin. Example configurations to set up custom Ensembl sites using GenomeHubs. GenomeHubs example configuration and demo scrip ...

Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies. The METATRYP software consists of:. METATRYP allows users to investigate the occurrence of tryptic peptides within the protein coding sequen ...

Gene Ontology Meta Annotator for Plants. Lawrence-Dill Plant Informatics and Computation Lab. Welcome to GOMAP-singularity’s documentation! — GOMAP-Singularity 1.3.2 documentation. All publications and products by the team at Lawrence-Dill Plant I ...