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Beginning Perl for Bioinformatics

Beginning Perl for Bioinformatics
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D
Data Bank of Japan (DBJ)

data bank or data store, databases vs.

data structures (complex), creating in Perl

data structures for biology
gene expression data
unsorted arrays, using for

relational databases

summary of

data, graphical representation of

databases
biological data

data banks or data stores vs.

database management

gene expression

PDB files
referenced in

relational
SQL (Structured Query Language)

DBI (Data Base Independence) module

DBM (database management)
database for GenBank

different implementations of

inadequacy for large projects

indexing GenBank with

restriction enzymes, storing in

dbmopen and dbmclose functions

DBREF record type, PDB files
example

debuggers

debugging
comments, use in

Mutate DNA program (example)

Perl debugger, using
use strict; and use warnings;

decimal numbers , 2nd

declaring
arrays

my variables
enforcing with strict pragma

variables
in loops

decrementing variables

defined and undefined values

defined function , 2nd

DEFINITION field, collecting in GenBank annotations

definitions of subroutines

dereferencing

designing programs
input and output

object-oriented programming

top-down vs. bottom up

die function

directives, printf function

directories, in different operating systems

disease treatment, protein structure and

divisions, GenBank libraries

DNA
bases
counting in strings

coding and noncoding

coding regions

concatenating fragments with join function

counting nucleotides in
tr function, using

cutting to insert a gene

mutations, investigating with randomization
random sequences, comparing bases for identity

reading from FASTA files

regulatory elements in, program to count

reverse complement of strands, calculating

separating from GenBank file annotations

sequences
storing in variables

transcribing to RNA

translating into amino acids and proteins
reading frames

writing formatted sequence data

DNA computers

do-until loops , 2nd , 3rd

do-while loops

documentation
BLAST

Perl
regular expressions

See : ., under Symbols dot (.) operator

double helix

downloading
code examples from this book

Perl

droplet, Macperl application

drugs, targeting proteins with