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File Formats in
Bioinformatics

Introduction
• To store biological data digitally, it requires specialised file formats to
represent the biological information of molecular sequences and
structures
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For example, web page was written on

an
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HTML files contain special tags that tell the
browser what each block of text is, and how to display it on the page
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Plain text formats
• Early databases stored sequence data in a file
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• More common file types include csv and tsv
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• Markdown format is a markup language , like HTML, it includes headers and paragraphs lines
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md in a source file from GitHub or Public Data repositories
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The Genbank file format is quite flexible and allows

annotations, comments, and references to be included within
the file
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Genbank files often have the file extension '
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genbank'
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Sample EMBL Format
ID AB000263 standard; RNA; PRI; 368 BP
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XX
SQ Sequence 368 BP;
acaattggccc………………………………………………
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• Text format file with extension
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• Originated from the sequence alignment software called
FASTP
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The identifier – comments, annotations
2
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Identifier

It is preceded by with a ">"
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Major database sequence identifiers are :

GenBank/EMBL/DDBJ
gi|gi_number|*|accession
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NCBI refseq
ref|accession|locus
SWISS-PROT

sp|accession|locus
PDB
pdb|entry|chain

2) Sequence
• Contains the raw sequence
• Standard nucleic acid and amino acid IUB/IUPAC codes are used
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fna - nucleic acid

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faa - aminoacids

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Sample Fasta format protein sequence
>gi|13959657|sp|Q9PTU8|VSP3_BOTJA Venom serine proteinase A precursor
MVLIRVIANLLILQLSNAQKSSELVIGGDECNITEHRFLVEIFNSSGLFCGGTLIDQEWVLSAAHCDMRN
MRIYLGVHNEGVQHADQQRRFAREKFFCLSSRNYTKWDKDIMLIRLNRPVNNSEHIAPLSLPSNPPSVGS
VCRIMGWGTITSPNATFPDVPHCANINLFNYTVCRGAHAGLPATSRTLCAGVLQGGIDTCGGDSGGPLIC
NGTFQGIVSWGGHPCAQPGEPALYTKVFDYLPWIQSIIAGNTTATCPP

FastQ Format – Delivered from Sequencers
1
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The second line is the raw sequence
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The third line starts with ‘+’ and can have the
same sequence identifier appended
4
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The BAM is a binary file format
while the SAM file format contains the same information but is text based
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Both the BAM/SAM format contain not only the sequence data
for next-generation sequencing reads, but also have the
capability of storing alignment data of those reads to a
reference sequence
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Alignment – read name, sequence, quality , alignment
information
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• It consists of one line per feature, each containing 3-12
columns of data
• User defined sequence features as well as graphical
representations of features
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3 required fields :
• Name of the chromosome or scaffold
• Start position of the feature in standard chromosomal coordinates
• End position of the feature in standard chromosomal coordinate
Chr1 21345679
21356739
9 optional fields :
• Label to be displayed under the feature
• A score between 0 and 1000
• defined as + (forward) or – (reverse)
• Thick start : the start codon for the gene display
• Thick end : Ending position of where the feature is drawn thickly
• itemRgb :Determines the color of the data contained in the BED line
• blockCount : the number of sub-elements \(e
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exons\) within the feature
• blockSizes : the size of these sub-elements
• blockStarts : the start coordinate of each sub-element

Protein Structure File Format
• PDB - the PDB file format is used to store both

sequence information, but more importantly stores 3dimensional structure information
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PDB files are simply text files, thus can be viewed with a
text editor, and often have the file extension '
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• HEADER: contains name and source of the protein,
resolution, description of experimental conditions and
details, names of the authors, crystallographic parameters
including R-factor, sequence information, secondary
structure information, literature citations etc
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• ATOM: this part contains the atomic coordinates and the Bfactor values as part of the protein chain
• HETATM: coordinates of cofactor molecules, substrates,
other groups that are not covalently bound to the protein
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The MDL mol
file contains information regarding 2d (and possibly 3d) molecule

structure, such as atom type and atom connectivity

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