Sequence Searching and Alignment

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Presentation transcript:

Sequence Searching and Alignment

https://www.ncbi.nlm.nih.gov/ Example: enolase

Scroll down…

Copy and paste the sequence, including the header to a text file.

Now get the sequence of the next organism and put it in the text file >gi|55229730|gb|AAV45149.1| enolase [Haloarcula marismortui ATCC 43049] MTLITDIRLRRVLDSRGNATVEADVLTESGGFGRGKAPSGASTGEYEAIELPANEAIAKAREEALPRLIG EVHAGNQRDVDAALHAADGTDDFSGIGANSAVAISMAAAKAGADVLGAPLYQHLGGTFRGNEYPTPLGNI IGGGEHAADATNIQEFLAAPVGAPSVEEAVFANAAVHQEVHDILADRDLPAGKGDEGAWAPSVSDDEAFE IMDEAVETVADDFGFAISFGLDVAGAELYDDEADGYVYDDGVKSTEEQIEYIAGKVEEYDLVYVEDPLDE NDYEAFADLTAQVGDQTLVCGDDLFVTNVERLQAGINADAGNSILIKPNQIGTLTDAVDAIELATASGYE SVVSHRSGETEDTTIAHLAVATDAPFIKTGAVGGERTAKLNELIRIEDNAV Edit the header of the file. Put part of the organism name into the first field and the enzyme name in the second field, as I have done below. Do not delete the vertical lines or add spaces. >gi|Haloarcula|enolase|AAV45149.1|enolase [Haloarcula marismortui ATCC 43049] MTLITDIRLRRVLDSRGNATVEADVLTESGGFGRGKAPSGASTGEYEAIELPANEAIAKAREEALPRLIG EVHAGNQRDVDAALHAADGTDDFSGIGANSAVAISMAAAKAGADVLGAPLYQHLGGTFRGNEYPTPLGNI IGGGEHAADATNIQEFLAAPVGAPSVEEAVFANAAVHQEVHDILADRDLPAGKGDEGAWAPSVSDDEAFE IMDEAVETVADDFGFAISFGLDVAGAELYDDEADGYVYDDGVKSTEEQIEYIAGKVEEYDLVYVEDPLDE NDYEAFADLTAQVGDQTLVCGDDLFVTNVERLQAGINADAGNSILIKPNQIGTLTDAVDAIELATASGYE SVVSHRSGETEDTTIAHLAVATDAPFIKTGAVGGERTAKLNELIRIEDNAV Now get the sequence of the next organism and put it in the text file

Repeat off of this until you have collected all your sequence data.

>gi|Haloarcula|enolase|AAV45149 >gi|Haloarcula|enolase|AAV45149.1|enolase [Haloarcula marismortui ATCC 43049] MTLITDIRLRRVLDSRGNATVEADVLTESGGFGRGKAPSGASTGEYEAIELPANEAIAKAREEALPRLIG EVHAGNQRDVDAALHAADGTDDFSGIGANSAVAISMAAAKAGADVLGAPLYQHLGGTFRGNEYPTPLGNI IGGGEHAADATNIQEFLAAPVGAPSVEEAVFANAAVHQEVHDILADRDLPAGKGDEGAWAPSVSDDEAFE IMDEAVETVADDFGFAISFGLDVAGAELYDDEADGYVYDDGVKSTEEQIEYIAGKVEEYDLVYVEDPLDE NDYEAFADLTAQVGDQTLVCGDDLFVTNVERLQAGINADAGNSILIKPNQIGTLTDAVDAIELATASGYE SVVSHRSGETEDTTIAHLAVATDAPFIKTGAVGGERTAKLNELIRIEDNAV >gi|Drosophila|enolase|AAV45149.1|[Drosophila melanogaster] MTIKAIKARQIYDSRGNPTVEVDLTTELGLFRAAVPSGASTGVHEALELRDNDKANYHGKSVLKAVGHVN DTLGPELIKANLDVVDQASIDNFMIKLDGTENKSKFGANAILGVSLAVAKAGAAKKGVPLYKHIADLAGN KEIILPVPAFNVINGGSHAGNKLAMQEFMILPTGATSFTEAMKMGSEVYHHLKNVIKAKFGLDATAVGDE GGFAPNIQSNKEALNLISDAIAKAGYTGKIEIGMDVAASEFYKDGQYDLDFKNEKSDKSQWLPADKLANL YQEFIKDFPIVSIEDPFDQDHWEAWSNLTGCTAIQIVGDDLTVTNPKRIATAVEKKACNCLLLKVNQIGT VTESIAAHLLAKKNGWGTMVSHRSGETEDSFIGDLVVGLSTGQIKTGAPCRSERLAKYNQILRIEEEIGA GVKFAGKSFRKPQ Put all of your sequences (with edited headers, together in one file and save it. Then go to an alignment program - T-coffee, Clustal, Muscle, etc

Paste your fasta sequences

submit

Aligned sequences

Paste Fasta file submit

Make a Distance tree

The following slides on the Needleman–Wunsch algorithm are from http://www.maths.tcd.ie/~lily/pres2/sld001.htm Aoife McLysaght Murfit Institute of Genetics University of Dublin, Trinity College Dublin 2 Ireland