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SEQUENCE FILE FORMATS

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introduction

Data is stored in a biological database in the form of sequences or molecular form

Unique file format Representation of data in biological

database Categories of file formats

Sequence database Molecular database

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Sequence file formats

Gene bank flat-file Format FASTA Format Multi-FASTA Format GCG Format GCG-MSF Format EMBL Format Clustal Format SWIS PROT format

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Gene bank flat-file Format

Used by NCBI It is divided into three parts Header just a direct and very precise

or brief introductory part Features

all genes in seq., location of genes in genome, protein product and coding genes etc. Sequence : ORIGIN atcgatcgatgcgctat

//

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Description of gene bank flat file identifiers

HEADRES Locus Definition Accession Version Dbsource: dates for creation and modifications Keywords Source Organism References Authors Title Journal Medline ID: all published sources Comment FEATURES SEQUENCE

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Retrieved from ncbi

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Fasta format

One line header Stats with > followed by name of gene Sequence of gene or protein

Blank spaces Paragraph marks Numerals

Are all ignored Steric sign * at the end

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FASTA Format

>p53 ctcgaggggc ctagacattg ccctccagag agagcaccca acaccctcca ggcttgaccg 61 gccagggtgt ccccttccta ccttggagag agcagcccca gggcatcctg cagggggtgc 121 tgggacacca gctggccttc aaggtctctg cctccctcca gccaccccac tacacgctgc 181 tgggatcctg gatctcagct ccctggccga caacactggc aaactcctac tcatccacga 241 aggccctcct gggcatggtg gtccttccca gcctggcagt ctgttcctca cacaccttgt 301 tagtgcccag cccctgaggt tgcagctggg ggtgtctctg aagggctgtg agcccccagg 361 aagccctggg gaagtgcctg ccttgcctcc ccccggccct gccagcgcct ggctctgccc*

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Multi-FASTA Format

Just like an aggregation of FASTA file as listed above

Multiple sequences follow one after the other

Single file Accepted by several databases Clustal W Multalin

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MULTI FASTA format

> jhumagccagggtgt ccccttccta ccttggagag agcagcccca gggcatcctg cagggggtgc >bhuma

gccagggtgt ccccttccta ccttggagag agcagcccca gggcatcctg cagggggtgc >puma

gccagggtgt ccccttccta ccttggagag agcagcccca gggcatcctg cagggggtgc >zuma

gccagggtgt ccccttccta ccttggagag agcagcccca gggcatcctg cagggggtgc

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GCG Format

GCG: genetics computer group First line says it all …. !!N.A_SEQUENCE 1.0 !!AA_SEQUENCE 1.0 Just a simple format in which we just

get to now the sequence for the genes or proteins

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GCG format

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GCG-MSF Format

Multiple sequences Sequence name Sequences Alignment Word pileup indicates that It is a multiple

sequence containing file Mandatory MSF word indicated in the file that

tells that it is an MSF GCG file and is not just GCG Comments terminated with // 2 consecutive blank lines Multiple sequences

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GCG MSF Format

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EMBL Format

Sequence format of European molecular biology laboratory database

Starts with ID identification number Ends with // as terminator Different lines with own format Used to record various forms of data i.e DNA, RNA, GENE, PROTEIN etc etc

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EMBLformat

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Clustal Format

Most widely used sequence alignment tool

CLUSTAL W CLUSTAL X Aligned protein or gene sequences

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Clustal x

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SWIS PROT format

Protein sequence database ID : identification number AC: accession number DE: description GN: gene name OS: organism specie OG: organelle OC: organism classification OX: organism taxonomy cross reference RN: reference number RP: reference position

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Continued…

RC: reference comment RX: reference cross reference RA: reference author RT: reference title RL: reference location CC: blank DR: database cross reference KW: key word FT: feature table SQ: sequence //

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Sequence conversion tools

Several software's have been designed by … ?

The aim of these software's is to make a detailed conversion of one sequence format into another

Some of the software used widely for sequence inter-conversion are :

ReadSeq GCG SeqVerter Seqret

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Read Seq

Developed by Dr. D.G Gilbert Automated conversion 18 supported file formats are there

which can be interconverted into one another

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Assignment

FASTA Multi FASTA Flat file GCG format EMBL Clustal SWISS PROT

Make each file by this Friday and send as attachments in an email 30

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Molecular file formats

continued…