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https://github.com/Brazelton-Lab/seq-annot
Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes.
Proper citation: seq-annot (RRID:SCR_018731) Copy
https://github.com/TransDecoder/TransDecoder
Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.
Proper citation: TransDecoder (RRID:SCR_017647) Copy
https://www.sanger.ac.uk/science/tools/reapr
Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.
Proper citation: Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) Copy
Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images.
Proper citation: QuPath (RRID:SCR_018257) Copy
https://github.com/taborlab/FlowCal
Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots.
Proper citation: FlowCal (RRID:SCR_018140) Copy
https://github.com/ComparativeGenomicsToolkit/hal/tree/master/synteny
Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment.
Proper citation: halSynteny (RRID:SCR_018127) Copy
https://github.com/almorlio/CiLiQuant
Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance.
Proper citation: CiLiQuant (RRID:SCR_019319) Copy
Database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them.
Proper citation: MyHits (RRID:SCR_006757) Copy
http://bioinformatics.biol.uoa.gr/cuticleDB
A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the five sequenced genomes where manual annotation has been applied to cuticular proteins: Anopheles gambiae, Apis mellifera, Bombyx mori, Drosophila melanogaster, and Nasonia vitripennis. Some sequences were confirmed as authentic cuticular proteins because protein sequencing revealed that they were present in cuticle; others were identified by sequence homology and other criteria. Entries provides information about whether sequences are putative or authentic cuticular proteins. CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin.
Proper citation: CuticleDB (RRID:SCR_007045) Copy
The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Users can BLAST sequences, browse by protein name, or view by protein function and functional subclass.
Proper citation: DisProt - Database of Protein Disorder (RRID:SCR_007097) Copy
A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions.
Proper citation: GBrowse (RRID:SCR_006829) Copy
A database of proteins identified by various 2-D PAGE and SDS-PAGE reference maps. Each SWISS-2DPAGE entry contains textual data on one protein, including mapping procedures, physiological and pathological information, experimental data (isoelectric point, molecular weight, amino acid composition, peptide masses) and bibliographical references. In addition to this textual data, SWISS-2DPAGE provides several 2-D PAGE and SDS-PAGE images showing the experimentally determined location of the protein, as well as a theoretical region computed from the sequence protein, indicating where the protein might be found in the gel. Using the database, users can locate these proteins on the 2-D PAGE maps or display the region of a 2-D PAGE map where one might expect to find a protein from UniProtKB/Swiss-Prot.
Proper citation: SWISS-2DPAGE (RRID:SCR_006946) Copy
http://www.agbase.msstate.edu/
A curated, open-source, web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. AgBase provides tools designed to assist with the analysis of proteomics data and tools to evaluate experimental datasets using the GO. Additional tools for sequence analysis are also provided. We use controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species. AgBase will also accept annotations from any interested party in the research communities. AgBase develops freely available tools for functional analysis, including tools for using GO. We appreciate any and all questions, comments, and suggestions. AgBase uses the NCBI Blast program for searches for similar sequences. And the Taxonomy Browser allows users to find the NCBI defined taxon ID for or taxon name for different organisms.
Proper citation: AgBase (RRID:SCR_007547) Copy
HubMed provides an interface to PubMed. Quick access to searches with a Firefox search plugin or a HubMed bookmarklet (drag to your browser''s bookmarks toolbar). Export citations in RIS, BibTeX, RDF and MODS formats, or directly to RefWorks. Unzip HubMed''s import filter into Endnote''s Filters folder for direct import into Endnote, or install the RIS Export plugin for direct import into ProCite, RefMan and older versions of Endnote. Use the Citation Finder to convert reference lists from PDFs into search results. Create lists of closely related papers using Rank Relations, then visualise and browse clusters of related papers using TouchGraph (requires Java). Graph occurrences of keywords in published papers over time. Tag and store annotated metadata for articles of interest.
Proper citation: HubMed (RRID:SCR_007296) Copy
COGEME is an ongoing BBSRC-funded study to construct a relational database of genomic information from phytopathogenic fungi. This site also hosts microarray data for Blumeria graminis. Expressed sequence tags (ESTs) obtained from eighteen species of plant pathogenic fungi, two species of phytopathogenic oomycete and three species of saprophytic fungi are included here. Hierarchical clustering software was used to classify together ESTs representing the same gene and produce a single contig, or consensus sequence. The unisequence set for each pathogen therefore represents a set of unique gene sequences, each one consisting of either a single EST or a contig sequence made from a group of ESTs. Unisequences were annotated based on top hits against the NCBI non-redundant protein database using blastx.
Proper citation: COGEME Phytopathogenic Fungi and Oomycete EST Database (RRID:SCR_007604) Copy
http://atlasgeneticsoncology.org/
Online journal and database devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. Its aim is to cover the entire field under study and it presents concise and updated reviews (cards) or longer texts (deep insights) concerning topics in cancer research and genomics.
Proper citation: Atlas of Genetics and Cytogenetics in Oncology and Haematology (RRID:SCR_007199) Copy
CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels: Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis Users can search CATH by ID/Sequence/text. They can also browse CATH from the top of the hierarchy, or download CATH data.
Proper citation: CATH: Protein Structure Classification (RRID:SCR_007583) Copy
http://bioinformatics.istge.it/cldb/indexes.html
Hypertext on cell culture availability extracted from the Cell Line Data Base of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue, and now also links to the PubMed, database of bibliographic biomedical references, which are drawn primarily from MEDLINE and PREMEDLINE.
Proper citation: Hyper Cell Line Database (RRID:SCR_007730) Copy
http://www.ebi.ac.uk/GenomeReviews/
THIS RESOURCE IS NO LONGER IN SERVICE, documented April 24, 2017. The Genome Reviews database provides an up-to-date, standardized and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota. Genome Reviews is available as a MySQL relational database, or a flat file format derived from that in the EMBL Nucleotide Sequence Database. An Ensembl-style browser is now available for Genome Reviews, providing a zoomable graphical view of all chromosomes and plasmids represented in the database. The location and structure of all genes is shown and the distribution of features throughout the sequence is displayed.
Proper citation: Genome Reviews (RRID:SCR_007685) Copy
http://firedb.bioinfo.cnio.es/
A database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords. FireDB contains information on every chemical compound in the PDB, including their descriptions, the PDB structures in which the compounds are found and the amino acids that are in contact with the ligand.
Proper citation: FireDB (RRID:SCR_007655) Copy
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