Timeline for Understanding PAM and BLOSUM matrices
Current License: CC BY-SA 3.0
13 events
| when toggle format | what | by | license | comment | |
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| Apr 25, 2017 at 21:04 | comment | added | David | Not at all. I don't answer questions in comments, so if others don't vote this as off-topic, I'll post a proper answer next week. (But anyone else is at liberty to spare me the chore.) | |
| Apr 25, 2017 at 15:54 | history | edited | tryingtolearn | CC BY-SA 3.0 |
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| Apr 25, 2017 at 15:44 | comment | added | David | The Wikipedia entries describe the data used for these matrices. As already commented, many pre-existing Protein (not DNA as in your question) sequences are needed and used to get a meaningful matrix. No, it isn't perfect, but your intuition is wrong — it works well enough. No, you can't use a matrix from two sequences, and especially two you are trying to align with a program that uses a matrix. Yes, you can modify standard matrices to get position-specific matrices as you perform multiple alignments of many sequences you already know are similar (see docs for Clustal). | |
| Apr 25, 2017 at 15:02 | history | edited | tryingtolearn | CC BY-SA 3.0 |
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| Apr 25, 2017 at 15:02 | review | Close votes | |||
| May 12, 2017 at 3:00 | |||||
| Apr 25, 2017 at 15:01 | comment | added | tryingtolearn | That answer only states how they're calculated not what data is used to calculate them nor does it discuss differences between matrices when using different query sequences, or intuition behind "lumping them together" which is what I'm after :/ | |
| Apr 25, 2017 at 14:58 | comment | added | tryingtolearn | @David Sorry, I don't think it's the same thing. I came across that topic and read it multiple times but it doesn't answer my question. | |
| Apr 25, 2017 at 14:44 | comment | added | David | Possible duplicate of biology.stackexchange.com/questions/49036/…. Please search for other questions on a topic on SE Biology. BLOSUM brings up several hits. | |
| Apr 25, 2017 at 14:42 | comment | added | David | Possible duplicate of Scoring matrices (BLOSUM & PAM) in BLAST and other sequence-comparison programs | |
| Apr 25, 2017 at 12:07 | comment | added | tryingtolearn | @JeppeNielsen There are multiple matrices as the matrix is generated based on the sequence that I'm querying? Or there are a few standard matrices that are used depending on the type of query? | |
| Apr 25, 2017 at 11:58 | comment | added | Jeppe Nielsen | There are multiple matrices. The matrices scores various mutations slightly different and the use of them depends on how big the evolutionary distance is expected to be among the sequences. (en.wikipedia.org/wiki/Point_accepted_mutation)(https://… | |
| Apr 25, 2017 at 11:57 | history | edited | tryingtolearn |
including bioinformatics tag
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| Apr 25, 2017 at 11:50 | history | asked | tryingtolearn | CC BY-SA 3.0 |