#BLAST COMPARE TWO PROTEIN SEQUENCES FREE#

this online EMBOSS-Explorer implementation. This is possible using an implementation of Needleman and Wunsch that allows you to use your own comparison matrix, e.g. In theory to get the highest identity score you should use a scoring matrix in which all perfect matches scored the same, and all mismatches zero. This is quite likely for sequences of 90% identity or higher, but there is no reason it should necessarily be the case. Now you would expect that the ‘best’ sequence alignment obtained by optimizing for similarity in this way would also give the best identity score. (More info on this and these terms can be found in the Wikipedia Sequence Alignment entry or in the BLAST Glossary.) Moreover, a perfect match for an amino acid like Trp scores much higher than one for Gly. Glu/Asp) may give a score of 4, compared with a perfect match score of 5. For example a match between similar amino acids (e.g. This is done by using one of a number of emperical scoring matrices that encompass the likelihood of particular amino acid substitutions. But these programs try to find the ‘best’ alignment not on the basis of the highest identity score, but on the basis of the highest similarity score. The patent says that “The optimal alignment is the alignment in which the percentage identity is the highest possible”. I do see one theoretical problem with these programs in relation to the patent, although this may not matter in practice. Alternatively, there is an implementation of the Needleman and Wunsch algorithm at NBCI, tucked misleadingly into the BLAST suite.

#BLAST COMPARE TWO PROTEIN SEQUENCES FREE#

You can find free web implementations of both of them at the EBI website (among other places) where the program ‘Needle’ performs the global alignment you require. From your patent specification you clearly want a global alignment and a value for percentage identity. So for pairwise comparison of two sequences one normally uses a program that implements the Smith and Waterman dynamic programming algorithm for local alignment (only the regions of best similarity are compared) or the Needleman and Wunsch algorithm for global alignment (the whole of both sequences are compared). Furthermore the output is not what you want as it scores a local alignment, whereas what your patent specifies is a global alignment ( see below). There is an option at the BLAST implementation at NCBI for just comparing two sequences, but this seems strange as one may as well just use the dynamic-programming alignment algorithm. Each of the highest scoring sequences obtained is ‘finished’ for presentation by running an implementation of quite different older and slower dynamic-programming algorithm, which is non-heuristic. BLAST is a program that uses heuristics for rapid searching of a large database for sequences similar to a query sequence. If you want to compare two specific sequences that you already have, then BLAST itself is not the program you need.

Blast compare two protein sequences