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How can i use BALIBASE to make comparison between (t-coffee,clustal,muscle)?step by step plz

How can i use BALIBASE to make comparison between (t-coffee,clustal,muscle)?step by step plz

alignment sequencing
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written by sallyzaki70 • sallyzaki70

2 answers

HI 1-i used the data set

>seq0
FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
>seq1
KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKKIEKFHSQLMRLME LKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq2
EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK
>seq3
MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK
>seq4
EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVVSYEMRLFGVQKDNFALEHSLL
>seq5
SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKKIEKLTTLLMR
>seq6
FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKKLEKLSSTLLRSI
>seq7
SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKKMEKLNNIFF
>seq8
SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq9
KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK
>seq10
FDSWDEFVSKSVELFRNHPDTTRYVVKYRHCEGKLVLKVTDNHECLKFKTDQAQDAKKMEK

2-used the online page of (clustal/t-coffee/muscle) to make MSA 3-get the output 4-then i used these outputs as an input in scorecones server i want to know the next step exactly how can i use BALIBASE to compare between (clustal/t-coffee/muscle) as i will draw a curve between the output of (clustal/t-coffee/muscle/balibase) the nearest one to balibase will be the best and where can i put the input (i want to work online)in balibase how can i align with BALIBASE Scorecons results for output of(clustal/t-coffee/muscle) , compared against BALiBASE scores.

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updated by WouterDeCoster WouterDeCoster • written by sallyzaki70 • sallyzaki70

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

Please spend some more time making your post easy to read. Currently, it's too hard to parse.

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written by WouterDeCoster WouterDeCoster

0.) Read How To Ask Good Questions On Technical And Scientific Forums

1.) read some background material (e.g. here, here, here, here)

2.) Download BALiBASE

3.) Install alignment programs

4.) Perform alignments with each alignment software

5.) Compute score for each alignment produced

6.) If getting errors: post new question, describing steps taken till tat point, commands used and error messages

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written by h.mon h.mon

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