Gene transfer format
File format for genomic features
The Gene transfer format (GTF) is a file format used to hold information about gene structure. It is a tab-delimited text format based on the general feature format (GFF), but contains some additional conventions specific to gene information. A significant feature of the GTF that can be validated: given a sequence and a GTF file, one can check that the format is correct. This significantly reduces problems with the interchange of data between groups.
GTF is identical to GFF, version 2.[1]
References
- ^ GFF/GTF info, from Ensembl
External links
- Info from UCSC Genome Bioinformatics Site
- Detailed GTF v2.2 Format Description
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Bioinformatics
- Sequence databases: GenBank, European Nucleotide Archive, DNA Data Bank of Japan and China National GeneBank
- Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource
- Other databases: BioNumbers, Protein Data Bank, Ensembl, InterPro, KEGG, and Gene Ontology
- Specialised genomic databases: BOLD, Saccharomyces Genome Database, FlyBase, VectorBase, WormBase, Rat Genome Database, PHI-base, Arabidopsis Information Resource, GISAID and Zebrafish Information Network
- Server: ExPASy
- Rosalind (education platform)
- Broad Institute
- Computational Biology Department (CBD)
- Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI)
- Database Center for Life Science (DBCLS)
- DNA Data Bank of Japan (DDBJ)
- European Bioinformatics Institute (EMBL-EBI)
- European Molecular Biology Laboratory (EMBL)
- Flatiron Institute
- J. Craig Venter Institute (JCVI)
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
- US National Center for Biotechnology Information (NCBI)
- Japanese Institute of Genetics
- Netherlands Bioinformatics Centre (NBIC)
- Philippine Genome Center (PGC)
- Scripps Research
- Swiss Institute of Bioinformatics (SIB)
- Wellcome Sanger Institute
- Whitehead Institute
- African Society for Bioinformatics and Computational Biology (ASBCB)
- Australia Bioinformatics Resource (EMBL-AR)
- European Molecular Biology network (EMBnet)
- International Nucleotide Sequence Database Collaboration (INSDC)
- International Society for Biocuration (ISB)
- International Society for Computational Biology (ISCB)
- Student Council (ISCB-SC)
- Institute of Genomics and Integrative Biology (CSIR-IGIB)
- Japanese Society for Bioinformatics (JSBi)
- Basel Computational Biology Conference ([BC2])
- European Conference on Computational Biology (ECCB)
- Intelligent Systems for Molecular Biology (ISMB)
- International Conference on Bioinformatics (InCoB)
- International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB)
- ISCB Africa ASBCB Conference on Bioinformatics
- Pacific Symposium on Biocomputing (PSB)
- Research in Computational Molecular Biology (RECOMB)
- CRAM format
- FASTA format
- FASTQ format
- NeXML format
- Nexus format
- Pileup format
- SAM format
- Stockholm format
- VCF format
- GFF format
- GTF format
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