Notes

Lecture3: Proteins
There are four protein structures. There is the primary structure, the secondary structure, the tertiary structure and the quaternary structure.

The primary structure is a sequence of amino acids held together by covalent bonds, normally represented by a string of characters. Each protein has a unique seqence that identifies it. The ends of of this sequence are reffered to as C-terminus and N-terminus.

Secondary structures are sub-structures in a large protein based on sequence. The first sub-sctructure is the hydropathy plot, which indetifies domains within a protein that are soluble or insoluable. Another sub-structure is the aplha helix, which is a group of amino acids with proteins that arrange themselves in a helical structure. The last sub-structure is the beta sheet, which is a group of amino acids within a protein that arrange themselves in a stable aligned (parralel) configuration.

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Alpha Helix https://upload.wikimedia.org/wikipedia/commons/e/ec/Alpha_helix_neg60_neg45_sideview.png

Tertiary Structure https://upload.wikimedia.org/wikipedia/commons/3/3d/1GZX_Haemoglobin.png
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Tertiary structures are the three dimensional representation of proteins where the alpha helixes and beta sheets are folded into a globalular structure.

Quaternary structures are the three dimensional structures of multi-subunit proteins and how they fit together. Tertiary structures may fold together into quaternary structure.

Lecture 4: Sequence Analysis
(PIC:
Sequence Alanysis
https://upload.wikimedia.org/wikipedia/commons/thumb/a/a7/WPP_domain_alignment.PNG/800px-WPP_domain_alignment.PNG
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Sequence analysis is determining how similar two or more gene/protein sequences are to eachother. This is a main function in bioinforrmatics since it is used for gene/protein identification, determining gene/protein function and for measuring genetic disease.
In Pair Wise analysis and Multple Sequence Alignments, the similarity measurement is computational and we can identify common regions of sequence identity and rank order multiple sequences to identify the sequences that are the most similar, or the genetic distance.
In Sequence Identification we compare a sequence of interest to a database of known sequences. With this, we identify those sequences tht are most similar to the sequence of interest.

(PIC:
Dynamic Programming
http://imgur.com/NRUjynG
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Dynamic Programming is a programming technique for solving combination problems. It is important in bioinformatics because it is the basis of sequence alignment algortiithims used for comparing protein and DNA sequences. It is used because of how efficient it is compared to simple recursive algortithms.
BLAST, or Basic Local Alignment Search Tool, is a widely used bioinformatics program for sequence searching. It works by preindexing all possible 11-letter words into a database. BLAST finds similar sequences by locating short matches between the two sequences. First, it finds all 11-letter words in the query sequence, then it looks up these in the index. After it retrieves all of the sequences containign those words, ti uses a rigourous algorithm to extend the match in both directions.