DNA > Biotech
Nucleic Acid Sequencing
Horses, MegaFLOPS and DNA
Sequencing
1. Sanger
method and automated sequencing
Sanger
sequencing - classic
Human Genome sequencing: "How to sequence a genome",
click on the animations nn. 6,
7,
8
and 9.
Electrophoretogram
Automated sequencing: features and problems. Troubleshooting.
2. Next
Generation Sequencing (NGS)
Editorial
(from "Focus
on DNA sequencing technology")
Overview
of NGS - NGS
Methods (Metzker 2010; Goodwin et al., 2016)
The Sequence Read Archive
(SRA) stores raw sequencing data from the next generation of
sequencing platforms
Example - Whole
Brain Human Transcriptome - SRX7397821:
GSM4222744: Human whole brain 3 - Reads
Sequence analysis
Bioinformatic Analysis
in Genomics: notes
Sequence
Alignment [pdf article]
Sequence
Search [pdf article]
Sequence comparison software:
BLAST
TAGCTAGCTAGCTAGCTAGCTAGCTAGC
TAGCTAGCTAGC-AGCTAGCTAGCTAGC
BLAST Parameters
BLOSUM62
Amino Acids Scoring Matrix - Negative scores prevail: substitutions
often negatively affect protein function.
TBLASTN - Amino Acids vs Nucleotides.
Example: RCAN1; vs RefSeq RNA; vs RefSeq Genome.
PSI-BLAST
Splign
SRA
- Sequence Read Archive
Example: Search SRA for: adult brain[Title] AND homo
sapiens[Organism] AND 2020/04/01:2020/06/01[PDAT]
Example: Search KCNJ6
E3-E4 boundary (last 25 bases of E3 + first 25 bases of E4) in
SRX8068355 via SRA BLAST
Protein domain search:
CDD
- SMART
[The small
bioinformatician]
FASTA FORMAT:
>Free text
cgcgcgctgcctgaggacgccgcggcccccgcccccgccatgggcgcccctgcctgcgccctcgcgctct...
DNA