sequence of file formats in bioinformatics

methods and tools

1. SEQUENCE FILE FORMATS 1

2. 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 2

3. 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 3

4. 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 // 4

5. 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 5

6. Retrieved from ncbi 6

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9. 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 9

10. 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 * 10

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12. 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 12

13. MULTI FASTA format > jhuma gccagggtgt 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 13

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15. 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 15

16. GCG format 16

17. 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 17

18. GCG MSF Format 18

19. 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 19

20. EMBL format 20

21. Clustal Format Most widely used sequence alignment tool CLUSTAL W CLUSTAL X Aligned protein or gene sequences 21

22. Clustal x 22

23. 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 23

24. 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 // 24

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26. 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 26

27. Read Seq Developed by Dr. D.G Gilbert Automated conversion 18 supported file formats are there which can be interconverted into one another 27

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30. 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

31. Molecular file formats continued… 31