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sequence of file formats in bioinformatics

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methods and tools

sequence of file formats in bioinformatics

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  2. 2.  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. 3.  Gene bank flat-file Format  FASTA Format  Multi-FASTA Format  GCG Format  GCG-MSF Format  EMBL Format  Clustal Format  SWIS PROT format 3
  4. 4.  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. 5.  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
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  9. 9.  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. 10.  >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 ccccggccct10
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  12. 12.  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. 13.  > 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. 15.  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
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  17. 17.  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
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  19. 19.  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
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  21. 21.  Most widely used sequence alignment tool  CLUSTAL W  CLUSTAL X  Aligned protein or gene sequences 21
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  23. 23.  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. 24.  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. 26.  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. 27.  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. 30.  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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