Thursday, April 25, 2013

An introduction to the command line

Week 1

Text file example - rhododendrons in Origin of Species (Right-click, save linked file):
http://www.gutenberg.org/cache/epub/1228/pg1228.txt

Today's Inspiration:
Is a short sequence motif (ex. a restriction site) located in a long sequence?
How many examples of that motif exist?
How many sequences exist that could mutate to become this restriction site? (for example, are one or two bases away from the motif)

Ngan's flanking sequence file (Click link to download):
Copia_Full_Element_Flank.fasta


grep -c -E ".TGCAG|C.GCAG|CT.CAG|CTG.AG|CTGC.G|CTGCA." Copia_Full_Element_Flank.fasta 
Posted by at

5 comments:

  1. UnknownMay 3, 2013 at 1:39 PM

    http://blast.ncbi.nlm.nih.gov/Blast.cgi or google "blast"


    EU528615.1

    ReplyDelete
  2. UnknownMay 3, 2013 at 1:54 PM

    Blast AY765980
    Then exclude Rhododendron (taxid:4346) and Blast AY765980

    ReplyDelete
  3. UnknownMay 3, 2013 at 1:58 PM

    Add Viridiplantae (taxid:33090) to avoid non plant hits.

    ReplyDelete
  4. UnknownMay 3, 2013 at 2:09 PM

    http://www.girinst.org/censor/index.php
    Repbase search

    ReplyDelete
  5. UnknownMay 3, 2013 at 2:19 PM

    TGTCGGAAGTCCAAACACTTCTACTTTTGAGCGCCAGATGGCACCACGCAGAAATGCGCAAATGTGAAGT
    CCCCGGCCTTACCATTTGTGCTGTAGGAGGCTCTTCCCCTTTATCTCTCTCTCTCCCTTTTTCATTGTTC
    TCACTCACGCGACGACCACGTTGCGAGAAGGTTCTCTCAGCAATCTGTATTTTAGTTCCTTTCATCTTTA
    GTTTTTCTCATTCAGAATCACTGGATCAAATTTATTCTTTCTTGTGAGAAATCGCTGTGTAATACTCAAC
    AACTGGTAATTACTTGTTTATCATTTCACGTATATGTAAATGTGCTACGTCTCCATTTCCCCCAGCAATA
    GAGTGTTATCACTTGAGCTCCGTTTATTCTTGTTACACATGTACCCGTCACGTGTTTATACAAATAATTT
    TCCACGTTGATCTCGTGATTCCCCTTATGTCGAATTATCACCATTGTCTAAGTTGATTCATTTTTGTCTC
    CACACATGTGGAAAGCCTGTTCTCAATACAGAAGCCTCTAAGTCGATTCTTTTGTTTCACGTGTATTTCC
    AACAGGTTATGGGCCCAGCACGTACCTGACTTGCTGAAACAAAATGAACTCAACGCTAAGAGAAGTGAGC
    CACATAGCCAAGTTCAATGGCACCAATTTCTCCCTATGGAAATTCGGAACATGGCTGTTACTAGAACAAC
    ACAATCTAGTTGGCATAGTAAATGGGGAGGAACTCTACCCTGAGGATGTAAGACTATTCTATCATACACA
    TGTTACCAACAGATGGTTTAATTCTTCACGTCAAATCCCTTTTTAGGAGATGATTGATGACGAGTTGGTC
    CCTCATGACGCAGAAAGGATGGATTGGATACGTAGAGATATCCTAGCCAGAAATTACCTCGTGGCCACGA
    TCGAAAGCCAACAGCAGAGGTCTCTGATCAATTGTCGCACGGCATACGAGATGTGGACACGCCTCTCAGC
    ACAACATCTCCGCAACGCCGTAGAGAATCAACACGTGCTCCAACAAAAATTCTTTGAATATCAGTACCAG
    CCAGAACATGACATCATGGCACACATTACTGAGGTGGAAACTATGGCGTCAATGCTAAGTGACGTGGAGG

    ReplyDelete

Subscribe to: Post Comments (Atom)