Introduction to Bioinformatics

Following sequencing, the two modalities of analysis are alignment to a reference genome and de novo assembly of reads into a genome sequence.

Any three major types of variants include single nucleotide polymorphisms (SNPs), insertions, and deletions.

Disease-specific variants are termed somatic variants.

The preferred tool for transcriptome assembly in de novo and genome-guided modalities is Trinity.

BLAT and BLAST are both used for sequence comparison, but they differ in speed and sensitivity. BLAT stores the genome index in memory and is designed to quickly find highly similar sequences (more than 95%), usually of at least 40 nucleotides. BLAST is used to search a nucleotide or protein query against a non-redundant sequence database and is more general-purpose for homology search.

Structural bioinformatics came first. The chapter says studies on protein three-dimensional structures using NMR spectroscopy and X-ray crystallography pre-date genome and other -ome informatics.