|Register||Search||Today's Posts||Mark Forums Read|
|Bioinformatics Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.|
| ||LinkBack||Thread Tools||Display Modes|
protein/DNA sequence alignment tool
can anybody please help me with the understanding of various algorithms used in the analysis of protein/DNA sequence alignment, in general?
what are the various algorithms commonly used ?
What all data base these algorithms use to generate data? I mostly work with human and mouse samples.
Thanks for the help!
Re: protein/DNA sequence alignment tool
Well there 2types:
1.local (Smith-waterman algorithm): Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context. The Smith-Waterman algorithm is a general local alignment method also based on dynamic programming. With sufficiently similar sequences, there is no difference between local and global alignments.
2.global(Needleman-Wunsch algorithm):Global alignments, which attempt to align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size. (This does not mean global alignments cannot end in gaps.) A general global alignment technique is the Needleman-Wunsch algorithm, which is based on dynamic programming.
u also have the pairwise (comparison of 2 sequences)and Multiple sequence alignment(comparison of more than 2 sequences)
just search on the web.. you have many resources like: NCBI,EBI,DDBJ,etc.
|alignment , protein or dna , sequence , tool|
|Thread||Thread Starter||Forum||Replies||Last Post|
|Human Cytome Project - Update 24 Jan. 2005||Peter Van Osta||Cell Biology and Cell Culture||1||08-01-2010 02:18 PM|
|Human Cytome Project - an idea - Update 19 April 2005||Peter Van Osta||Cell Biology and Cell Culture||1||06-01-2009 02:17 PM|
|Sequence alignment from BLAST output||Mark Nance||Protocols and Methods Forum||1||09-17-2008 05:41 AM|
|A Human Cytome Project - an idea - Update 14 March 2005||Peter Van Osta||Cell Biology and Cell Culture||0||03-14-2005 01:27 PM|
|Human Cytome Project - Update 6 Jan. 2005||Peter Van Osta||Cell Biology and Cell Culture||0||01-06-2005 10:18 AM|