Module 2: Storage, Retrieval and Manipulation of DNA Information (General Themes)
How to manipulate DNA sequences for various applications? (Elaborated in subsequent lectures)
|Similarity searches for a newly identified sequence: New DNA information identified from any source (organism, tissue, disease,
etc.) can be queried for similarity in structure (and hence, maybe function) to already published sequences in database(s). There
are a variety of techniques to search for similarities between sequences (Module 4). Each of
these methods has its merits and demerits based on the nature of the algorithms used, the stringency requirements of the researcher
performing the search, the format of the queried database, and the type(s) of outputs generated.
Alignments of sequences: When two or more sequences are aligned they can show local or global similarity(ies) which may infer
functional homologies in the polypeptides encoded within the sequences (Module 5). Some of the
available computing software allow the intentional placement of gaps in the sequences (gapping) to arrive at optimal alignments.
- Pairwise: When two sequences are aligned with same or similar data values over short or long stretches of DNA the
algorithms work fairly well. The two sequences can be aligned by searching for localized regions of similarity between them
(local alignment) or aligned globally over the whole sequences
(global alignment). A computing technique called "dynamic
programming" is utilized to obtain the optimal alignment between the 2 sequences.
- Multiple: When more than two sequences are to be aligned a multiple alignment algorithm has to be invoked. Such alignments
are performed mostly for localization of consensus sequences at the nucleic acid or protein level. In general, a multiple alignment
is done as an incremental process wherein pairwise alignments are initially performed and then new sequences are added one at a
time. Multiple alignments can be done in a local or global setting.
Structure-function relationships: There are not many direct applications of structure-function relationships with DNA sequence
alone. We will discuss (Module 6) the computational analysis of regulatory roles of DNA sequences
involved in replication, transcription, transpositions, and chromosomal functions (eg., centromeres and telomeres in chromosomal
duplication and cell division).