Practical’s

Submitted By:
Kainat Yaseen
F22BMLTH1E01011
5th Semester
Bioinformatics

Submitted To:
Dr. Arslan Sehgal

THE ISLAMIA UNIVERSITY OF

BAHAWALPUR
 Practical No. 1

Use of bioinformatics software for

Data analysis of PTEN gene
National center of biotechnology
information (NCBI)
PROTEIN DATA BANK (PDB)
ENSEMBL
KYOTO ENCYCL OF GENE AND GENOME
(KEGG)
UNIPROT
UCSC GENOME BROWSER
STRING
GENE CARD
EUORPEON MOLECULAR BIOTECHNOLOGY
INFORMATION (EMBL)
OMIM
 Practical No. 2

Function:
The PTEN gene (Phosphatase and Tensin Homolog) is a tumor suppressor that regulates cell
growth, division, and survival by deactivating the PI3K/AKT signaling pathway. It plays a critical role in
preventing uncontrolled cell proliferation, which can lead to cancer. Mutations in PTEN are associated
with various cancers and genetic disorders like Cowden syndrome.

METHODLOGY
1) Search uniprot database.
2) Search desired gene i.e. PTEN.
3) Go to sequences and isoform tab.
4) Copy sequence of gene.
5) Search BLAST and open it.
6) Then click on protein BLAST.
7) Paste sequences copied from uniprot.
8) Click BLAST.
9) Here are the sequences
10) Open any of 4 or 5 accessions in new window by clicking on
accession number.

11) After clicking accession this interface comes.

12) Now click on FASTA.

13) Then this sequences comes.

14) Copy this sequences.
15) Open clustal Omega.
16) Paste all sequences.
 Practical No. 3

Multiple sequences
alignment result

Submit CLUSTAL OMEGA result.

CLUSTAL O(1.2.4) multiple sequence alignment

XP_051056030.1 MDTLGRRAYTRPVCTIVVLGWGRSFISRANDPSRLGSKRWGREPEPAKHCSLTTAQGRQG
60
XP_048192451.1 ------------------------------------------------------------
0
XP_042545373.1 ------------------------------------------------------------
0
XP_069876606.1 ------------------------------------------------------------
0

XP_051056030.1 MLAPSKEAQGRRQDGCPCRRALPLGLQTLASAASWPDAPLSSQRSCSAQLPSVTAFPTLA
120
XP_048192451.1 ------------------------------------------------------------
0
XP_042545373.1 ------------------------------------------------------------
0
XP_069876606.1 ------------------------------------------------------------
0

XP_051056030.1 GSPRRGRKPAQLPETTAATLGMLGGRRSPPRPAGAPPRPAPPPPRLGPPARLPLSCRLPS
180
XP_048192451.1 ------------------------------------------------------------
0
XP_042545373.1 ------------------------------------------------------------
0
XP_069876606.1 ------------------------------------------------------------
0

XP_051056030.1 RLPRRPALLAGRRRGRAGRPAHGDVAGLFVHCGRIRAWASGRGCAELSPLGSCSHDGTAA
240
XP_048192451.1 ---------------------------------------------------------AAA
3
XP_042545373.1 ---------------------------------------------------------AAA
3
XP_069876606.1 ---------------------------------------------------------AAA
3
:**

XP_051056030.1 GAAPSGSRPGGGG--------------------------SGSGSGGGPRL-LVVYSNRAA
273
XP_048192451.1 GAAPSGSRPACSGGGSRSSTSSSSS----------TTSSSSGGGGGVPRLLSAVFSNRAA
53
XP_042545373.1 GAAPSGSRPACGGGGSRSSPSSSSSSSSS--SSSTSSSSSGGGGGGVPRLLSAVFSNRAT
61
XP_069876606.1 GAAPSGSRPACGGGGSRSSPSSSSSSSSSSSSSSTSSSSGGGGGGGVPRLLSVVFSNRAA
63
*********. .* ...*.** *** .*:****:

XP_051056030.1 SERLRRETDGGSRGLGREPAHAR-RLHLPLLERVGEAAAA------AAAAPGRGSESPVT
326
XP_048192451.1 SASASPARHGGHRGPRREPAEARRRRHLPLLERGGEAAAAAAAAAAAAPAPGRGSEPPVT
113
XP_042545373.1 SSSASAARDGGRRGPGREPAAARRRRHLPLLERGGEAAAAAAAAAAAAPAPGRGSEPPVT
121
XP_069876606.1 SSSASAARDGGRRGPGREPAAARRRRHLPLLERGGEAAAAAAAAAAAAPAPGRGSEPPVT
123
* .** ** **** ** * ******* ****** ** ******* ***

XP_051056030.1 IARAGNAGELLSPLLLPPTRRRRRRHVQGPGPVLSLPSAAAAPPLARAPEAAGGGSRCCE
386
XP_048192451.1 ISRAGDAGELVSPLLLPPTRRRRRRRIQGPGPVLNLPSAAAALPLARAPEAAGGGSR-SE
172
XP_042545373.1 ISRAGDAGELVSPLLLPPTRRRRRRRIPGPGPVLNLPSAAAALPLARAPEAAGGGSR-SE
180
XP_069876606.1 ISRAGDAGELVSPLLLPPTRRRRRRRIPGPGPVLNLPSAAAALPLARAPEAAGGGSR-SE
182
*:***:****:**************:: ******.******* ************** .*

XP_051056030.1 DYPSSPHSAASAARPLAAEEKQAQSLQPSSS------------------SSRRSSHYPAA
428
XP_048192451.1 DYSSSAHSAAAAARPLAAEEKQASPLQPSSSSSSSGSSSS---GSNSSSSRRRSSHYPAA
229
XP_042545373.1 DYSSSAHSAAAAARPLAAEEKQASSLQPSSSSSSSGSSSSSGSSSSSSSSRRRSSHYPAA
240
XP_069876606.1 DYSSSAHSAAAAARPLAAEEKQASSLQPSSSSSSSGSSSSSS-SSGSSGSRRRSSHYPAA
241
** ** ****:************. ****** * *********

XP_051056030.1 VQGQAAAERGASATAKSRAVSILQKKPRHQQLLPSLSSFFFSHRLPDMTAIIKEIVSRNK
488
XP_048192451.1 VQSQAAAERGASATAKSRAISILQKKPRHQQLLPSLSSFFFSHRLPDMTAIIKEIVSRNK
289
XP_042545373.1 VQSQAAAERGASATAKSRAISILQKKPRHQQLLPSLSSFFFSHRLPDMTAIIKEIVSRNK
300
XP_069876606.1 VQSQAAAERGASATAKSRAISILQKKPRHQQLLPSLSSFFFSHRLPDMTAIIKEIVSRNK
301
**.****************:****************************************

XP_051056030.1 RRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAE
548
XP_048192451.1 RRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAE
349
XP_042545373.1 RRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAE
360
XP_069876606.1 RRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAE
361
************************************************************

XP_051056030.1 RHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGV
608
XP_048192451.1 RHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGV
409
XP_042545373.1 RHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGV
420
XP_069876606.1 RHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGV
421
************************************************************

XP_051056030.1 MICAYLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVAL
668
XP_048192451.1 MICAYLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVAL
469
XP_042545373.1 MICAYLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVAL
480
XP_069876606.1 MICAYLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVAL
481
************************************************************

XP_051056030.1 LFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDI
728
XP_048192451.1 LFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDI
529
XP_042545373.1 LFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDI
540
XP_069876606.1 LFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDI
541
************************************************************

XP_051056030.1 KVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGSLCDQEIDSICSIERADNDK
788
XP_048192451.1 KVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGSLCDQEIDSICSIERADNDK
589
XP_042545373.1 KVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGSLCDQEIDSICSIERADNDK
600
XP_069876606.1 KVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGSLCDQEIDSICSIERADNDK
601
************************************************************

XP_051056030.1 EYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNE
848
XP_048192451.1 EYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNE
649
XP_042545373.1 EYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNE
660
XP_069876606.1 EYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNE
661
************************************************************

XP_051056030.1 PDHYRYSDTTDSDPENEPFDEDQHSQITKV 878

XP_048192451.1 PDHYRYSDTTDSDPENEPFDEDQHTQITKV 679
XP_042545373.1 PDHYRYSDTTDSDPENEPFDEDQHTQITKV 690
XP_069876606.1 PDHYRYSDTTDSDPENEPFDEDQHTQITKV 691
************************:*****