Keywords and Expertise
Use keywords to characterize workflows and forum posts, and reach out to sellers with relevant expertise
JavaScript Object Notation format; a lightweight, text-based format to represent tree-structured data using key-value pairs.
Common Workflow Language (CWL) format for description of command-line tools and workflows.
bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format.
Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information.|The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database.
FASTQ short read format ignoring quality scores.
Tabular data represented as comma-separated values in a text file.
BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.
The Zarr format is an implementation of chunked, compressed, N-dimensional arrays for storing data.
Entry format of PDB database in PDB format.
The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound.|An InChIKey identifier is not human- nor machine-readable but is more suitable for web searches than an InChI chemical structure specification.
SDF is one of a family of chemical-data file formats developed by MDL Information Systems; it is intended especially for structural information.
FASTA format including NCBI-style IDs.
The Terse RDF Triple Language (Turtle) is a human-friendly serialisation format for RDF (Resource Description Framework) graphs.|The SPARQL Query Language incorporates a very similar syntax.
FASTQ Illumina 1.3 short read format.
SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language for querying and manipulating data stored in Resource Description Framework (RDF) format.
Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.|The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project.
Tabular data represented as tab-separated values in a text file.
GFF feature format (of indeterminate version).
Gene Transfer Format (GTF), a restricted version of GFF.
FASTQ short read format with phred quality.
Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).
Reference-based compression of alignment format
SRA archive format (SRA) is the archive format used for input to the NCBI Sequence Read Archive.
The BIological Observation Matrix (BIOM) is a format for representing biological sample by observation contingency tables in broad areas of comparative omics. The primary use of this format is to represent OTU tables and metagenome tables.|BIOM is a recognised standard for the Earth Microbiome Project, and is a project supported by Genomics Standards Consortium. Supported in QIIME, Mothur, MEGAN, etc.
Biological Dynamics Markup Language (BDML) is an XML format for quantitative data describing biological dynamics.
Textual format.|Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual).
Format of a hidden Markov model representation used by the HMMER package.
Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation.
Biological Connection Markup Language (BCML) is an XML format for biological pathways.
Affymetrix data file format for information about experimental conditions and protocols.
Data format for raw data from a nuclear magnetic resonance (NMR) spectroscopy experiment.
The XYZ chemical file format is widely supported by many programs, although many slightly different XYZ file formats coexist (Tinker XYZ, UniChem XYZ, etc.). Basic information stored for each atom in the system are x, y and z coordinates and atom element/atomic number.|XYZ files are structured in this way: First line contains the number of atoms in the file. Second line contains a title, comment, or filename. Remaining lines contain atom information. Each line starts with the element symbol, followed by x, y and z coordinates in angstroms separated by whitespace. Multiple molecules or frames can be contained within one file, so it supports trajectory storage. XYZ files can be directly represented by a molecular viewer, as they contain all the basic information needed to build the 3D model.
BioJSON is a BioXSD-schema-based JSON format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web applications and APIs, and object-oriented programming.
Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters.
Cytoband format for chromosome cytobands.|Reflects a UCSC Browser DB table.
Data format for raw microarray data.
Human ENCODE narrow peak format.|Format that covers both the broad peak format and narrow peak format from ENCODE.
GNU zip compressed file format common to Unix-based operating systems.
A profile (sequence classifier) in the format used in the JASPAR database.
Codata entry format.
A standardized file format for data exchange in mass spectrometry, initially developed for infrared spectrometry.|JCAMP-DX is an ASCII based format and therefore not very compact even though it includes standards for file compression.
The GEN file format contains genetic data and describes SNPs.
Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database.
The file format for MATLAB scripts or functions.
Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema.
Alphabet for molecular sequence with possible unknown positions but without non-sequence characters.
NeXML is a standardised XML format for rich phyloinformatic data.
Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package.