# comparison of several genomic regions with BLAST

**URL:** <https://community.alliancegenome.org/t/comparison-of-several-genomic-regions-with-blast/3672>\
**Category:** WormBase\
**Created:** [May 1, 2010, 4:13am UTC](https://community.alliancegenome.org/t/comparison-of-several-genomic-regions-with-blast/3672 "2010-05-01T04:13:51Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Antonio\_Tucci](https://community.alliancegenome.org/letter_avatar_proxy/v4/letter/a/eada6e/32.png) [@Antonio\_Tucci](https://community.alliancegenome.org/u/Antonio_Tucci)\
**Post date:** [May 1, 2010, 4:13am UTC](https://community.alliancegenome.org/t/comparison-of-several-genomic-regions-with-blast/3672/1 "2010-05-01T04:13:51Z")

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I’d like to know how to compare several genomic regions (i.e. 18S of a group of nematodes) … in order to see which sequences are common.

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**Author:** ![mh6](https://community.alliancegenome.org/letter_avatar_proxy/v4/letter/m/e495f1/32.png) [@mh6](https://community.alliancegenome.org/u/mh6)\
**Post date:** [July 20, 2010, 4:15pm UTC](https://community.alliancegenome.org/t/comparison-of-several-genomic-regions-with-blast/3672/2 "2010-07-20T16:15:10Z")

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one idea would be to use the C.elegans sequences as seeds and try to pull homolg sequences from GenBank/DDBJ/ENA … but you might want to realign the sequences, as blast can be a bit crude, but ymmv

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**Author:** ![luvkashyap](https://community.alliancegenome.org/letter_avatar_proxy/v4/letter/l/bbe5ce/32.png) [@luvkashyap](https://community.alliancegenome.org/u/luvkashyap)\
**Post date:** [July 20, 2010, 7:28pm UTC](https://community.alliancegenome.org/t/comparison-of-several-genomic-regions-with-blast/3672/3 "2010-07-20T19:28:35Z")

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Hi  
You can align the sequences using this Programme called “Clustal W” at [http://www.ebi.ac.uk/Tools/clustalw2/index.html](http://www.ebi.ac.uk/Tools/clustalw2/index.html)

From this you can get the common region/sequence of similarity

Hope this helps… 🙂

Luv

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**Author:** ![mh6](https://community.alliancegenome.org/letter_avatar_proxy/v4/letter/m/e495f1/32.png) [@mh6](https://community.alliancegenome.org/u/mh6)\
**Post date:** [July 23, 2010, 3:06pm UTC](https://community.alliancegenome.org/t/comparison-of-several-genomic-regions-with-blast/3672/4 "2010-07-23T15:06:06Z")

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have a look at

The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies  
, Patrick Schloss PLoS Comput Biol, Vol. 6, No. 7. (8 July 2010), e1000844.

[http://dx.doi.org/doi:10.1371/journal.pcbi.1000844](http://dx.doi.org/doi:10.1371/journal.pcbi.1000844)

for some pitfalls