Bioinformatics Exercises
  B.Computer. Unix
  Writer : Seyeon Weon   Updated : 10-14   Hit : 2286   Updates 

(For those who have taken the courses and want to submit for evaluation, please read the instructions linked on the table of contents page.)

  1. Grep and Regular Expression:

    Read the help documents by issuing "man grep" and "info grep". Download prosite database (http://www.expasy.org/prosite/) from ftp://bio-mirror.kr.apan.net/pub/biomirror/prosite/. Using grep, find out how many entries are in the database. How many "PATTERN" entries and how many "MATRIX" entries are in the database?

    Grep all "PATTERN"s from the database. Among them, how many of them have more than two occurrences of tyrosine.

    You may need to use "wc". Also, try to use pipe.

  2. GNU textutils:

    Read documents at http://www.gnu.org/software/textutils/manual/textutils/textutils.html. Grep values from prosite.dat for "total", "true positive", "false positive", and "false negative" using "grep" and "cut". Create 4 files, one for each category. Paste these 4 files into a single file using "paste".

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