Nussinov algorithm is an algorithm to predict possible RNA secondary structure (folding), discovering parts that have complementary sequences. Unlike search algorithms, this method works with the singlesequence. It computes the sequence against itself using dynamic programming table, however the matching scores are set so that the letters are treated as "matching" if the corresponding nucleotides would pair. Hence A "matches" U and G "matches" C, but none of the four (AGTC) nucleotides matches itself as two identical nucleotides do not pair.
2. Nussinov Algorithm:
Four ways to get the optimal structure between position iand j from the optimal substructure
Types of BLAST programs
There are five different blast programs, which can be distinguished by the type of the query sequence (DNA or protein) and the type of the subject database:
BLASTP compares an amino acid query sequence against a protein sequence database;
BLASTN compares a nucleotide query sequence against a nucleotide sequence database;
BLASTX compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database;
TBLASTN compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).
TBLASTX compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.
There are many databases to use as subject databases. One of the most commonly used is nr database: collection of "non-redundant" sequences from GenBank and other sequence databanks. For other subject databases available click here.
BLAST accept the sequence in FASTA format (see different formats we discussed last post) or Accession Number (GI number).
Parameters to adjust
EXPECT value: The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance. If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Increasing the EXPECT value forces the program to report less isgnificant matches.
FILTER (Low-complexity):Mask off segments of the query sequence that have low compositional complexity (i.e. regions of biased composition, such as short-period repeats)
For BLAST first-time user tutorial click here. For more advanced one click here.