Bioinformatics Tutorials (Lesson 4):Using ClustalW to do a multiple sequence alignment

[gigiatbsashtrance]

why on earth I can't use this shit??? DO i HAVE TO PAY TO USE IT???

[Slashgj88]

hi friend...how i can do a phylogenetic tree with clustalw? @Htheshadow

[Htheshadow]

@Slashgj88 , Hello, the tree that comes with ClustalW result page is not an actual phylogenetic tree, it's just a guide tree that helps ClustalW do the alignment, so be careful and don't use it as a phylogenetic tree, if you want to know how to generate a phylogenetic tree for your multiple sequence alignment, go to my video: Bioinformatics Tutorials (Lesson 9) Part 1:Using PHYLIP to build phylogenetic trees

[Slashgj88]

@Slashgj88 thanks!!!

[Slashgj88]

hi friend...how i can do a phylogenetic tree with clustalw?

[tumpiliksye]

how can you identify a position on an alignment generated by ClustalW that can be improved manually ?

[editormmc]

@tumpiliksye 1-Save your alingnment as a.aln file. (I prefer to use Muscle)

2-Open Jalview and RTFM

3-Open your saved alignment

4-Edit manually.

5-Saved as a new edited file

[umerfarooq2]

Hi sir, I'm a final year student of BS with majors in computer science. I'm interested in making my final year project in the field of bioinformatics. Can u give me some suggestions/ideas for the project?

[tolu2010]

Thank you, it helps just just i'm a new starter in bioinformatics, you knw it's kind of hard for me to understand. i will appreciate any suggestion to help. thanks.

[tolu2010]

i appreciate ur tutorial, it helps a lot. pls wat is the meaning of critical residue and how do i identify it.

[karadjic1]

Hi mate, A critical residue (amino acid) is one that has a very important role for that particular protein. you will not be able to find this simply by looking at the alignments from clustalw2.clustalw2 will show you a number of highly conserved residues which are all important, so in order to find out the critical one, you need to read published journals about your protein

[karadjic1]

if and when you find the journal, look for amino acids that constitute the active site of your protein, as critical residues are almost always the ones that make up the active site and make sure to note the position of this critical residue eg. threonine 75. then once you know the position too, download rasmol(three dimensional program)allows you to view the 3d structure of a protein and using the tools available look for the critical residue at that position and anotate it. I hope this helps