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Useful links for Problem Set: BioPerl BioPerl BLAST Command Line Applications User Manual Preparation (from command line):   1. Download uniprot_sprot:   curl -O "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"   2. Unzip the file.   gunzip uniprot_sprot.fasta.gz     PROBLEM 1: Bio::DB::Fasta   1. write a script to retrieve all IDs from uniprot_sprot.fasta using the Bio::DB:Fasta method: $db->get_all_primary_ids  … (read more)

Files, etc for Problem Set X: Statistics::Descriptive module Microarray.pm Perl X Problem Set ==================== 1. Take a look at the Statistics::Descriptive module on cpan. 2. Write a script that uses the methods in Statistics::Descriptive to calculate the standard deviation, median, min, and max of the following numbers:   12,-13,-12,7,11,-4,-12,9,6,7,-9   Optional questions:   3.Add a… (read more)

Perl IX: References Problem Set   Pre Questions:   P1. Create an array, retrieve the reference(address), print the reference(address). my @array = (‘a’ , 123, ‘book’ , ‘end’); P2. Use the reference to print out the 2nd and 3rd elements. P3. Create a hash, retrieve the reference (address), print the reference. P4. Use the reference… (read more)

Perl VIII – Modules – Problem Set   1. Download and install a module using CPAN   $ cpan   CPAN should ask if you want to configure automatically. Say YES. Once it’s done configuring, you should get a cpan prompt like this:   cpan>   Type the following to install the module Math::Round:  … (read more)

Subroutines and Scope, Perl VII Problem Set Perl VII Problem Set ===================== 1. Create a subroutine that reverse complements a sequence. This subroutine should take a nucleotide sequence as a parameter and return the reverse complement.   Here’s the pseudo code:   — BEGIN PSEUDOCODE —   subroutine reverse_complement {   get the parameter nucleotide… (read more)