Biological data

Biological data are data or measurements collected from biological sources, which are often stored or exchanged in a digital form. Biological data are commonly stored in files or databases. Examples of biological data are DNA base-pair sequences, and population data used in ecology.

Data File Formats

Each file format has been designed for specific needs and outputs in mind.

• GFF
• BAM
• SAM
• VCF
• AB1 – In DNA sequencing, chromatogram files used by instruments from Applied Biosystems
• ACE – A sequence assembly format
• BAM – Binary compressed SAM format
• BED – The browser extensible display format is used for describing genes and other features of DNA sequences
• CAF – Common Assembly Format for sequence assembly
• EMBL – The flatfile format used by the EMBL to represent database records for nucleotide and peptide sequences from EMBL databases
• FASTA – The FASTA file format, for sequence data. Sometimes also given as FNA or FAA (Fasta Nucleic Acid or Fasta Amino Acid).
• FASTQ – The FASTQ file format, for sequence data with quality. Sometimes also given as QUAL.
• GenBank – The flatfile format used by the NCBI to represent database records for nucleotide and peptide sequences from the GenBank and RefSeq databases
• GFF – The General feature format is used for describing genes and other features of DNA, RNA and protein sequences
• GTF – The Gene transfer format is used to hold information about gene structure.
• NEXUS – The Nexus file encodes mixed information about genetic sequence data in a block structured format.
• NWK – The Newick tree format is a way of representing graph-theoretical trees with edge lengths using parentheses and commas. It is useful to hold phylogenetic trees.
• PDB – structures of biomolecules deposited in Protein Data Bank. Also used for exchanging protein/nucleic acid structures.
• PHD – Phred output, from the basecalling software Phred
• SAM – Sequence Alignment/Map format, in which the results of the 1000 Genomes Project will be released.
• SCF – Staden chromatogram files used to store data from DNA sequencing
• SBML – The Systems Biology Markup Language is used to store biochemical network computational models
• SFF - Standard Flowgram Format
• Stockholm – The Stockholm format for representing multiple sequence alignments
• Swiss-Prot – The flatfile format used to represent database records for protein sequences from the Swiss-Prot database
• VCF – Variant Call Format, a standard created by the 1000 Genomes Project that lists and annotates the entire collection of human variants (with the exception of approximately 1.6 million variants).

Biological Data Sharing

• Genomics data sharing
• TransPLANT data

See also

• Bioinformatics
• Biological database
• Biological model (disambiguation)
• Data modeling
• DNA sequencing
• Data mining