Substitution matrices are used to score aligned positions in a sequence alignment procedure, usually of amino acids or nucleotide sequences.
Two commonly used matrices: PAM and BLOSUM
Two commonly used matrices: PAM and BLOSUM
- PAM = Percent Accepted Mutations (Margaret Dayhoff)
- BLOSUM = Blocks Substitution Matrix (Steven and Henikoff)
PAM VS BLOSUM
PAM
|
BLOSUM
|
| PAM matrices are used to score alignments between closely related protein sequences. | BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences. |
| Based on global alignments | Based on local alignments |
| Alignments have high similarity than BLOSUM alignments | Alignments have low similarity than PAM alignments |
| Mutations in global alignments are vey significant | based on highly conserved stretches of alignments |
| Higher numbers in the PAM matrix naming denotes greater evolutionary distance | Higher numbers in the BLOSUM matrix naming denotes higher sequence similarity and smaller evolutionary distance |
| Example: PAM 250 is used for more distant sequences than PAM 120 | Example: BLOSUM 80is used for closely related sequences than BLOSUM 62 |
Good narration. Helps me lot, thanks):
ReplyDeleteSo Helpful. Answered my question in less than a minute.
ReplyDeletethank you so much :D
ReplyDeleteReally Appreciated. Thank you!
ReplyDeleteAwesome! Fast and precise! :D
ReplyDeleteVery helpful..thank you so much
ReplyDeleteThank you so much. so helpful
ReplyDeleteThank you so much. it's so helpful.
ReplyDeleteyup.. thts right...Thanx anyways
ReplyDeleteNandrigal pala
ReplyDeletedanke schkon
ReplyDeletemodda gudpichu ra lanja
ReplyDeleteReally helpful Soo simple Thanks
ReplyDelete