Talk:Harvard:Biophysics 101/2007/02/13: Difference between revisions
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==Sequence-level differences to consider== | |||
*Point mutations | *Point mutations | ||
**silent/synonymous | **silent/synonymous | ||
| Line 12: | Line 12: | ||
**We should be able to determine AUG and stop codons... | **We should be able to determine AUG and stop codons... | ||
== | ==General coding questions / ideas== | ||
*How should we handle file input? | *How should we handle file input? | ||
*How should we format the output? | *How should we format the output? | ||
*Generation of a set of test inputs. | *Generation of a set of test inputs. | ||
*How can the identification of a class of differences be identified with a set of implementable conditions (ie how do you seperate out a duplication or an insertion from a rearrangement. | *How can the identification of a class of differences be identified with a set of implementable conditions (ie how do you seperate out a duplication or an insertion from a rearrangement. | ||
* | |||
==Using clustalw for sequence alignment== | |||
*[http://www.cf.ac.uk/biosi/research/biosoft/Downloads/clustalw.html clustalw] can be used for performing multiple sequence alignments | |||
*BioPython provides a wrapper for clustalw through the Bio.Clustalw package. However, clustalw needs to be downloaded and installed before it is accessible using your biopython scripts. | |||
*As [[User:Zsun|Zsun]] noticed, the [http://www.bioinformatics.org/bradstuff/bp/tut/Tutorial003.html BioPython cookbook] has some outdated example code for accessing clustalw. An online [http://www.pasteur.fr/recherche/unites/sis/formation/python/ch11s06.html Python Course in Bioinformatics] by Katja Schuerer and Catherine Letondal has several better examples with correct code. | |||
Revision as of 15:35, 19 February 2007
Sequence-level differences to consider
- Point mutations
- silent/synonymous
- missense
- nonsense
- translational stability (re: codon bias)?
- Deletions (and insertions)
- frame shift
- downstream effects?
- Add more here...
- Coding vs nonCoding seq
- We should be able to determine AUG and stop codons...
General coding questions / ideas
- How should we handle file input?
- How should we format the output?
- Generation of a set of test inputs.
- How can the identification of a class of differences be identified with a set of implementable conditions (ie how do you seperate out a duplication or an insertion from a rearrangement.
Using clustalw for sequence alignment
- clustalw can be used for performing multiple sequence alignments
- BioPython provides a wrapper for clustalw through the Bio.Clustalw package. However, clustalw needs to be downloaded and installed before it is accessible using your biopython scripts.
- As Zsun noticed, the BioPython cookbook has some outdated example code for accessing clustalw. An online Python Course in Bioinformatics by Katja Schuerer and Catherine Letondal has several better examples with correct code.
