The Genome Access Course Electronic Sequences

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TheGenomeAccessCourseElectronic Sequences
Insulin, sequenced in 1955
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This is a sequence

• MALWTRLRPLLALLALWPPPPARAFVNQHLCGSHLVEALYLVCGERGFFY
  TPKARREVEGPQVGALELAGGPGAGGLEGPPQKRGIVEQCCASVCSLYQL
  ENYCN

So is this
ACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGGCTGCATTCGAGGC
TGCCAGCAAGCAGGTCCTCGCAGCCCCGCCATGGCCCTGTGGACACGCCT
GCGGCCCCTGCTGGCCCTGCTGGCGCTCTGGCCCCCCCCCCCGGCCCGCG
CCTTCGTCAACCAGCATCTGTGTGGCTCCCACCTGGTGGAGGCGCTGTAC
CTGGTGTGCGGAGAGCGCGGCTTCTTCTACACGCCCAAGGCCCGCCGGGA
GGTGGAGGGCCCGCAGGTGGGGGCGCTGGAGCTGGCCGGAGGCCCGGGCG
CGGGCGGCCTGGAGGGGCCCCCGCAGAAGCGTGGCATCGTGGAGCAGTGC
TGTGCCAGCGTCTGCTCGCTCTACCAGCTGGAGAACTACTGTAACTAGGC
CTGCCCCGACAAATAAACCCTTACGAGCAAG
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Where do sequences come from?

• Individual researchers
• Genome sequencing projects
• Patent applications

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Where do the sequences go?

• GenBank (NCBI)
• EMBL Nucleotide Sequence Database
• DDBJ (DNA Data Bank of Japan)

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How can sequences be obtained?

• ENTREZ
• Batch ENTREZ
• SRS (Sequence Retrieval System)
• getentry

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What is available in Entrez?

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

• OMIM
• Taxonomy
• Books
• ProbeSet
• 3D Domains

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ENTREZ Cross-references
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Sequence Formats

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

• DDBJ
• Ensembl
• Graphics
• XML

- convertible in ReadSeq
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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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How to work with sequences

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

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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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ENTREZ Filters

• nucleotide allFilter NOT specimen-voucherAll
  Fields
• You can eliminate most of the BAC-type records
  from the default nucleotide database with the
  following query nucleotide allFilter NOT
  htgKeyword