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titleRun ClustalW

$ /home/<user>/clustalw-2.1-binary/bin/clustalw2 sample.fasta

CLUSTAL 2.1 Multiple Sequence Alignments

 

Sequence format is Pearson

Sequence 1: A4_Baboon    320 aa

Sequence 2: A4_Cattle    319 aa

Sequence 3: A4_Rabbit    319 aa

Start of Pairwise alignments

Aligning...

 

Sequences (1:2) Aligned. Score:  89

Sequences (1:3) Aligned. Score:  73

Sequences (2:3) Aligned. Score:  72

Guide tree file created:   [sample.dnd]

 

There are 2 groups

Start of Multiple Alignment

 

Aligning...

Group 1: Sequences:   2      Score:6615

Group 2: Sequences:   3      Score:5898

Alignment Score 4752

 

CLUSTAL-Alignment file created  [sample.aln]

 

Check the result:

$ ls -l

-rw-rw-r-- 1 farhan farhan   1747 Mar 10 09:34 sample.aln

-rw-rw-r-- 1 farhan farhan     60 Mar 10 09:34 sample.dnd

-rw-rw-r-- 1 farhan farhan   1041 Mar 10 09:34 sample.fasta

 

Check the content of the result:

$ cat sample.aln

CLUSTAL 2.1 multiple sequence alignment

 

 

A4_Baboon       MTMSSFLINSNYIEPKFPPFEEYAQHSGPGGEDGGPGGGPGYQQPPAPPTQHLPP--QQP

A4_Cattle       MTMSSFLINSNYIEPKFPPFEEYAQHSGPGGGDGGPGGGPGYQQPPAPAAQHLPPPQQQP

A4_Rabbit       MTMSSFLINSNYIEPKFPPFEEYAQHSGPGGGDGGPGGGPGYQQPPAPASQHRPP--QQP

                ******************************* ****************.:** **  ***

 

A4_Baboon       QLPHAGGGREPPASYYAPRTAREPAYPAAALYPSHRAADTAYPYGYRGGASPGRPPQPEQ

A4_Cattle       QLSHAGGSREPPASYYAPRAARESSYPAAALYPAHGAADTAYPYGYRGGASPGQPPQPEQ

A4_Rabbit       PLPHAGGSREPPATLLRAAGHPRARLPRGRALPRARCRGHRLPLWLPRRRQPRAAASARA

                 *.****.*****:   .    ..  * .   *   . .   *       .*  .....

 

A4_Baboon       PLAHAKGP-AHGLHASHVLQPQPPPPLQPRAVPPAAPRRCEAAPATPGVPAGGSAPACPL

A4_Cattle       PPAHAKAP-AHGLHASHVL---PPPPPQHRAAAPAPQRRCEAAPATPGVPSGGSAPACPL

A4_Rabbit       APGARQGPRARPAREPRPAAWPAAAAAAHRAAPPAPPRRCEAAPATPGVPAGGSAPACPL

                . .  :.* *:  : .:     ....   **..**. *************:*********

 

A4_Baboon       LLADKSPLGLKGKEPVVYPWMKKIHVSAVNPSYNGGEPKRSRTAYTRQQVLELEKEFHFN

A4_Cattle       LLADKSPPGLKGKEPVVYPWMKKIHVSAVNPSYNGGEPKRSRTAYTRQQVLELEKEFHFN

A4_Rabbit       LLADKSPPGLKGKEPVVYPWMKKIHVSAVNPSYNGGEPKRSRTAYTRQQVLELEKEFHFN

                ******* ****************************************************

 

A4_Baboon       RYLTRRRRIEIAHTLCLSERQVKIWFQNRRMKWKKDHKLPNTKMRSSNSASASAGPPGKA

A4_Cattle       RYLTRRRRIEIAHTLCLSERQVKIWFQNRRMKWKKDHKLPNTKMRSSNSGSASAGPPGKP

A4_Rabbit       RYLTRRRRIEIAHALCLSERQVKIWFQNRRMKWKKDHKLPNTKMRSTN--SASTGQPGKA

                *************:********************************:*  ***:* ***.

 

A4_Baboon       QTESPHLHPHPHPSTSTQVPSSI

A4_Cattle       QTQSPHLHPQPHQGASALTPSSM

A4_Rabbit       QTQSPHPHPHPVPGASTPIPSTI

                **:*** **:*  .:*:  **::

 

$ cat sample2.dnd

(

A4_Baboon:0.04702,

A4_Cattle:0.05956,

A4_Rabbit:0.21944);

 

 

Binary/Package Manager

To be continued....