BIOINFORMATIC TOOLS: I SHOULD MASTER THIS

Assalamualaikum wbt..
Today is my second class of CADD..
I supposed to enter last Tuesday class, but I was just having my wisdom tooth operation on Monday, thus I didn't come to class. Since my friend said that I should not miss this class for this week, I decided to enter the other section. Fortunately, there are a lot of section for this subject. 5 sections all.

Alright, for today class, Dr. Linda had taught us 4 bioinformatics tools.
1) BLAST
2) InterProScan
3) Catalytic Site Atlas (CAS)
4) Multiple Sequence Alignment (MSA)

BLAST

BLAST can help you to find 3 results from your sequence:
i) conserve domain
ii) graph
iii) alignment

Our PDB ID is 2HT5 (according to last class assignment)

Copy the FASTA sequence in Notepad (copy from Protein BLAST) > alter

Paste FASTA and choose PSI-BLAST for algorithm

Wait a few seconds. It is loading.
And you will get this result.

Query Seq is the sequence that we paste before, and it shows with green triange the catalytic sites.
Sialidase is the conserve domain (i) which is the other name of neuraminidase (2H5T).

Graph (ii) can be obtained by clicking on the red line.

2) InterProScan

InterProScan4 has similar function with BLAST but it is more details that you will be surprised when you found out that you actually have 2 conserved domain on your sequence!

Here the steps:

>Start with IPR

>Enter FASTA sequence (protein only)

>Submit

 
3) Catalytic Site Atlas (CAS)

CAS is a tool use basically to search active site on your sequence.
I'll expalin this on next post okay! Multiple Sequence Alignment (MSA) okay? Need to hurry. Bus is coming!

Wallahualam...:)

SBM4021

Assalamualaikum WBT

Computer Aided Drug Design Class brings me to this wall again. Heh~

Can't believe that it has been 4 years already

This was what we did today. Mesmerizing KOS1110 class back in 2010. :)

 N8 Neuraminidase
Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8)

•>EMBOSS_001

•ACCTACATGAACAACACCGAGGCCATCTGCGACGCCAAGGGCTTCGCCCCCTTCAGCAAGGACAACGGCATCAGGATCGGCAGCAGGGGCCACATCTTCGTGATCAGGGAGCCCTTCGTGAGCTGCAGCCCCATCGAGTGCAGGACCTTCTTCCTGACCCAGGGCAGCCTGCTGAACGACAAGCACAGCAACGGCACCGTGAAGGACAGGAGCCCCTTCAGGACCCTGATGAGCGTGGAGGTGGGCCAGAGCCCCAACGTGTACCAGGCCAGGTTCGAGGCCGTGGCCTGGAGCGCCACCGCCTGCCACGACGGCAAGAAGTGGATGACCGTGGGCGTGACCGGCCCCGACAGCAAGGCCGTGGCCGTGATCCACTACGGCGGCGTGCCCACCGACGTGGTGAACAGCTGGGCCGGCGACATCCTGAGGACCCAGGAGAGCAGCTGCACCTGCATCCAGGGCGACTGCTACTGGGTGATGACCGACGGCCCCGCCAACAGGCAGGCCCAGTACAGGATCTACAAGGCCAACCAGGGCAGGATCATCGGCCAGACCGACATCAGCTTCAACGGCGGCCACATCGAGGAGTGCAGCTGCTACCCCAACGACGGCAAGGTGGAGTGCGTGTGCAGGGACGGCTGGACCGGCACCAACAGGCCCGTGCTGGTGATCAGCCCCGACCTGAGCTACAGGGTGGGCTACCTGTGCGCCGGCATCCCCAGCGACACCCCCAGGGGCGAGGACACCCAGTTCACCGGCAGCTGCACCAGCCCCATGGGCAACCAGGGCTACGGCGTGAAGGGCTTCGGCTTCAGGCAGGGCACCGACGTGTGGATGGGCAGGACCATCAGCAGGACCAGCAGGAGCGGCTTCGAGATCCTGAGGATCAAGAACGGCTGGACCCAGACCAGCAAGGAGCAGATCAGGAAGCAGGTGGTGGTGGACAACCTGAACTGGAGCGGCTACAGCGGCAGCTTCACCCTGCCCGTGGAGCTGAGCGGCAAGGACTGCCTGGTGCCCTGCTTCTGGGTGGAGATGATCAGGGGCAAGCCCGAGGAGAAGACCATCTGGACCAGCAGCAGCAGCATCGTGATGTGCGGCGTGGACTACGAGGTGGCCGACTGGAGCTGGCACGACGGC GCCATCCTGCCCT

•>2HT5:A|PDBID|CHAIN|SEQUENCE

•TYMNNTEAICDAKGFAPFSKDNGIRIGSRGHIFVIREPFVSCSPIECRTFFLTQGSLLNDKHSNGTVKDRSPFRTLMSVE VGQSPNVYQARFEAVAWSATACHDGKKWMTVGVTGPDSKAVAVIHYGGVPTDVVNSWAGDILRTQESSCTCIQGDCYWVMTDGPANRQAQYRIYKANQGRIIGQTDISFNGGHIEECSCYPNDGKVECVCRDGWTGTNRPVLVISPDLSYRVGYLCAGIP SDTPRGEDTQFTGSCTSPMGNQGYGVKGFGFRQGTDVWMGRTISRTSRSGFEILRIKNGWTQTSKEQIRKQVVVDNLNWS GYSGSFTLPVELSGKDCLVPCFWVEMIRGKPEEKTIWTSSSSIVMCGVDYEVADWSWHDGAILPFDIDKM

Ok..What is this?? To be continue..........