Intro to Bioinformatics

1.     Basic molecular biology: central dogma

 http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology

    

       DNA:

                     

RNA:

                 

Protein:

                 

2.     NCBI

The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.

http://www.ncbi.nlm.nih.gov/

3.     Sequence Databases
Primary sequence repositories: GenBank (USA), EMBL (Europe) & DDBJ (Japan)

http://www.ncbi.nlm.nih.gov/genbank

       http://www.ebi.ac.uk/embl/

http://www.ddbj.nig.ac.jp/

Each of the three groups collects a portion of the total sequence data reported worldwide, and all new and updated database entries are exchanged between the groups on a daily basis.

4.     DNA sequencing and Next generation sequencing

http://en.wikipedia.org/wiki/DNA_sequencing

5.     Get familiar with sequence format.

Fasta: http://en.wikipedia.org/wiki/FASTA_format

Fastq: http://en.wikipedia.org/wiki/FASTQ_format

Genbank: http://quma.cdb.riken.jp/help/gbHelp.html

6.     Sequence alignment

              http://en.wikipedia.org/wiki/Sequence_alignment

7.     Blast: Basic Local Alignment Search Tool

http://en.wikipedia.org/wiki/BLAST
Tutorial: http://www.ncbi.nlm.nih.gov/books/NBK21097/

8.     Taxonomy
http://en.wikipedia.org/wiki/Biological_classification
Tutorial: http://www.ncbi.nlm.nih.gov/books/NBK53758/

9.     Programming Strategies in Bioinformatics

·       Avoid programming

·       Don’t change other people’s code… too much!

·       Reuse, Reuse, Reuse!

·       Wrappers on available tools.

·       Comment copiously

·       There is more than one way to do it!