TGAC Electronic Sequences

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TGACElectronic Sequences
Insulin, sequenced in 1955
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This is a sequence

• MALWTRLRPLLALLALWPPPPARAFVNQHLCGSHLVEALYLVCGERGFFY
  TPKARREVEGPQVGALELAGGPGAGGLEGPPQKRGIVEQCCASVCSLYQL
  ENYCN

This is also a sequence
ACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGGCTGCATTCGAGGC
TGCCAGCAAGCAGGTCCTCGCAGCCCCGCCATGGCCCTGTGGACACGCCT
GCGGCCCCTGCTGGCCCTGCTGGCGCTCTGGCCCCCCCCCCCGGCCCGCG
CCTTCGTCAACCAGCATCTGTGTGGCTCCCACCTGGTGGAGGCGCTGTAC
CTGGTGTGCGGAGAGCGCGGCTTCTTCTACACGCCCAAGGCCCGCCGGGA
GGTGGAGGGCCCGCAGGTGGGGGCGCTGGAGCTGGCCGGAGGCCCGGGCG
CGGGCGGCCTGGAGGGGCCCCCGCAGAAGCGTGGCATCGTGGAGCAGTGC
TGTGCCAGCGTCTGCTCGCTCTACCAGCTGGAGAACTACTGTAACTAGGC
CTGCCCCGACAAATAAACCCTTACGAGCAAG
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How to work with sequences

• Cut paste sequences
• Save files as text from sequence repositories
• Unix vs. Windows format

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How to Use Notepad

• Start Accessories Click Notepad
• Start Run Type notepad Click OK

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How to Use Cut and Paste on PCs

• Select sequence
• Hit Ctrl c to copy
• Hit Ctrl v to paste
• These options are also available through the Edit
  menu of most programs

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Whence come sequences?

• Individual researchers
• Genome sequencing projects
• Patent applications

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Whither do the sequences go?
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(No Transcript)
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How can sequences be obtained?

• Batch ENTREZ

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What is available via Entrez?

• PubMed
• Protein
• Nucleotide
• Structure
• Genome
• PopSet
• OMIM

• Taxonomy
• Books
• ProbeSet
• 3D Domains
• UniSTS
• SNP
• CDD

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ENTREZ XRefs Then
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ENTREZ XRefs Now
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Sequence Formats

• Raw
• Fasta
• ASN.1
• GenBank/GenPept

• DDBJ
• Ensembl
• Graphics
• XML

- convertible via ReadSeq
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Fasta Format
Greater than
No Whitespace!
Description line

• gtgi23200275pdb1KP5B Chain B, Cyclic Green
  Fluorescent Protein TGSRHHHHHHSRKGEELFTGVVPILVELDG
  DVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFXVQCFS
  RYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNR
  IELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIE
  DGSVQLADHYQQNTPIGDGPVLLPDNHYLS TQSALSKDPNEKRDHMVLL
  EFVTAAGLVPRGTGLYK

Line feed
Sequence in single-letter code
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GenBankFormat
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Graphics Format
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RefSeqs

• Reference sequence standards
• Available for chromosomes, mRNAs, proteins
• Non-redundant
• Curated
• Status and history are available
• Avoids redundancy in GenBank

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Nomenclature

• NW_ whole genome shotgun assembly
• NT_ BAC based contig
• NM_ Reference transcript
• XM_ Predicted transcript
• NP_ Referrence protein
• XP_ Predicted protein
• NC_ Reference chromosome(including mitchondrial
  and chloroplast genomes)

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Other Sequence Formats

• GCG
• DNA Strider
• Intelligenetics
• NBRF

- convertible in ReadSeq
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Multiple Sequence Formats

• MSF
• Phylip
• PAUP
• Fitch
• Pretty

- convertible in ReadSeq
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Converting Sequence Formats

• READSEQ
• SEQIO
• GCG e.g. FROMEMBL, TOFASTA, etc.

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Batch ENTREZ

• A method for obtaining large numbers of
  sequences by supplying a file containing a list
  of GI or accession numbers.

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Charles Babbage
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(No Transcript)
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(No Transcript)