methods and tools

1. 1

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
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3.  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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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 //
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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
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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
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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.  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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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.  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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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.  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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21.  Most widely used sequence alignment tool
 CLUSTAL W
 CLUSTAL X
 Aligned protein or gene sequences
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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.  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.  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.  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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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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