Computational Systems Biology Methods and Protocols.7z

The key to data analysis is data mining, of which the basis is

sequence similarities. The most common approach to similarity

research is DNA sequence alignment which can find the optimal

match between sequences according to similar matrix given, as well

as probable insertion, deletion, and mutation.

3.1.1 Two Stages of DNA
Sequence Analysis

Analyzing nucleic acid sequences with computer programs can be

divided into two stages:

1. The first stage is the straightforward search for sequences with
   known properties, which involves position determination.


2. The second stage aims to detect subtle, less straightforward
   sequence patterns including controlling elements like promo-
   ters. The results can be presented by catalogs of sequence
   patterns.

3.1.2 Two Categories of
Computational Approaches

Computational approaches to sequence alignment generally fall

into two categories: global alignments and local alignments.

1. Calculating a global alignment is a form of global optimization
   that “forces” the alignment to span the entire length of all
   query sequences.


2. Local alignments identify regions of similarity within long
   sequences that are often widely divergent overall. Local

Table 2
Several tools for data analysis

Function Name Site

Plot ggplot2 http://docs.ggplot2.org/current/

circos http://circos.ca/

Mapping BWA http://bio-bwa.sourceforge.net/

Bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

SNP/indel calling samtools http://samtools.sourceforge.net/samtools.shtml

gatk http://www.broadinstitute.org/gatk/

pindel http://gmt.genome.wustl.edu/pindel/0.2.4/index.html

Analysis tools plink http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml

ngsTools https://github.com/mfumagalli/ngsTools

Structure analysis frappe http://med.stanford.edu/tanglab/software/frappe.html

structure http://pritchardlab.stanford.edu/structure.html

ngsAdmix http://www.popgen.dk/software/index.php/NgsAdmix

Databases DDBJ http://www.ddbj.nig.ac.jp/index-e.html

ENA http://www.ebi.ac.uk/ena/home

KEGG http://www.genome.jp/kegg/

ensembl http://asia.ensembl.org/index.html

DNA Sequencing Data Analysis 9