Difference between revisions of "DNA sequence comparison"
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'''DNA sequence comparison''' is component of [[molecular pathology]]. | '''DNA sequence comparison''' is component of [[molecular pathology]]. | ||
==Using BLAST== | ''DNA sequencing'' redirect here. | ||
==Nomenclature== | |||
This is still somewhat in flux.<ref name=pmid17251329>{{cite journal |author=Ogino S, Gulley ML, den Dunnen JT, Wilson RB |title=Standard mutation nomenclature in molecular diagnostics: practical and educational challenges |journal=J Mol Diagn |volume=9 |issue=1 |pages=1–6 |year=2007 |month=February |pmid=17251329 |pmc=1867422 |doi=10.2353/jmoldx.2007.060081 |url=http://moldiag.highwire.org/cgi/content/full/9/1/1#B6}}</ref> | |||
==Data format== | |||
'''FASTA''': This contains just DNA sequence. The first line starts with '>' and contains the record name. | |||
'''FASTQ''': This contains DNA sequence data with quality scores: The quality scores are indicated by defined characters. | |||
==Basic local alignment search tool== | |||
*[[AKA]] BLAST. | |||
===Using BLAST=== | |||
#Go to BLAST web site ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ). | #Go to BLAST web site ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ). | ||
#Enter sequence. | #Enter sequence. | ||
#Enter consensus sequence. | #Enter consensus sequence (can be found with [[OMIM]]). | ||
#Hit enter. | #Hit enter. | ||
==See also== | ==See also== | ||
*[[Molecular pathology]]. | *[[Molecular pathology]]. | ||
*[[Channelopathies]]. | |||
*[[Decendent identification]]. | |||
*[[Next generation sequencing]]. | |||
==References== | |||
{{Reflist|1}} | |||
==External links== | ==External links== | ||
*[http://www.sanger.ac.uk/resources/software/act/ Artemis Comparison Tool (ACT) - a GPL'ed sequence comparison tool (sanger.ac.uk)]. | *[http://www.sanger.ac.uk/resources/software/act/ Artemis Comparison Tool (ACT) - a GPL'ed sequence comparison tool (sanger.ac.uk)]. | ||
*[http://en.wikipedia.org/wiki/List_of_sequence_alignment_software List of sequence alignment software (WP)]. | |||
*[http://blast.ncbi.nlm.nih.gov/Blast.cgi BLAST - sequence comparison tool (ncbi.nlm.nih.gov)]. | *[http://blast.ncbi.nlm.nih.gov/Blast.cgi BLAST - sequence comparison tool (ncbi.nlm.nih.gov)]. | ||
[[Category:Molecular pathology]] | [[Category:Molecular pathology]] | ||
Latest revision as of 19:39, 11 October 2023
DNA sequence comparison is component of molecular pathology.
DNA sequencing redirect here.
Nomenclature
This is still somewhat in flux.[1]
Data format
FASTA: This contains just DNA sequence. The first line starts with '>' and contains the record name.
FASTQ: This contains DNA sequence data with quality scores: The quality scores are indicated by defined characters.
Basic local alignment search tool
- AKA BLAST.
Using BLAST
- Go to BLAST web site ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ).
- Enter sequence.
- Enter consensus sequence (can be found with OMIM).
- Hit enter.
See also
References
- ↑ Ogino S, Gulley ML, den Dunnen JT, Wilson RB (February 2007). "Standard mutation nomenclature in molecular diagnostics: practical and educational challenges". J Mol Diagn 9 (1): 1–6. doi:10.2353/jmoldx.2007.060081. PMC 1867422. PMID 17251329. http://moldiag.highwire.org/cgi/content/full/9/1/1#B6.