File Formats

File formats

A list of bioinformatics file formats used by the Holmes lab

• Fasta format: DNA, amino acid and RNA sequences
• Stockholm format: multiple sequence alignments
• Newick format: phylogenetic trees
• Genome annotation:
  • Gff format & Bed format: co-ordinates and types of genes & other localized elements
  • Wig format: quantitative high-throughput experimental measurements on genomes

• xrate format: phylo-grammars

• Stanford format: tab-delimited format for microarray data

• Databases
  • Genbank format: sequences and annotation
  • Uniprot: protein sequences
  • Homstrad database: structural alignments
  • Pandit database: protein-coding gene alignments

• Ontologies, controlled vocabularies, whatever you wish to call them
  • Gene ontology
  • Sequence ontology
  • Bio Ontologies

File format conversion tools

• Stockholm tools
• Gff tools
• Mercator perl tools