Exercise 7

Exercise 7

Search Gene sequence and understand file formats in databases

(follow up of exercise 3 )

• Search the sequence of insulin from NCBI
• Save in FASTA and GenBank format
• Discuss entries and labels
• Locate all features - and write them down to understand
• Search CDS/protein record
• Compare fFASTA and GenBank format
• Search and download same sequence file from EBI-EMBL and DDBJ and compare formats

B Part

Convert Non-FASTA into FASTA format

• Since most sequence tools expect FASTA format, a “dirty” sequence (one with extraneous characters) can pose a problem
• The Sequence Manipulation Suite (SMS) is a tool that can be used to clean up such a sequence
• SMS can be found at http://www.bioinformatics.org/sms2
• Convert GenBank into FASTA
  • Open http://www.bioinformatics.org/sms2/genbank_fasta.html
  • Paste your GenBank File and press submit
  • It will give you FASTA sequence