Assignment: Multiple sequence alignment

Submitted by: Maham Wazir Zaadi

Submitted to: Mam Layla Sehar

Registration Number: 04282313023

Department: Bioinformatics Semester:

 MULTIPLE SEQUENCE ALINGMENT (MSA)

1#

Sequence 1: EFGR

Sequence 2: BRCA1

Sequence 3: TP53
CLUSTAL 2.1 Multiple Sequence Alignments

Sequence type explicitly set to DNA

Sequence format is Pearson
Sequence 1: EFGR 210 bp
Sequence 2: BRCA1 210 bp
Sequence 3: TP53 193 bp
Start of Pairwise alignments
Aligning...

Sequences (1:2) Aligned. Score: 15.2381

Sequences (1:3) Aligned. Score: 22.7979
Sequences (2:3) Aligned. Score: 20.7254
Guide tree file created: [clustalw.dnd]

There are 2 groups

Start of Multiple Alignment

Aligning...
Group 1: Delayed
Group 2: Delayed
Alignment Score 1204

CLUSTAL-Alignment file created [clustalw.aln]

clustalw.aln

CLUSTAL 2.1 multiple sequence alignment

EFGR GTTCGTTGCAACAAATTGATGAGCAATGCTTTTTTATAATGCCAACTTTGTACAAAAAAG
TP53 -----------TGGGTTGAT--TCCACACCCCCGCCCGGCACCCGCGTC-CGCGCCGTGG
BRCA1 -----------CCTAACCCTAACCCATAACCCTAACCCTAACCTACCCT-AACCCTAACC
* * * ** * *

EFGR TTGGCACCATGCGACCCTCCGGGACGGCCGGGGCAGCGCTCCTGGCGCTGCTGGCTGCGC
TP53 CCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGA----GGCGCTGC---CCCCAC
BRCA1 CTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA---CCCTAA
* * * * * * ** *

EFGR TCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAGTTTGCCAAGGCACGAGTAACAAGC
TP53 CATGAGCGCTGC-TCAGATAGCGATTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGT
BRCA1 CCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCTAACCCTAACCCTAACCCTAAAC
* * ** * *

EFGR TCACGCAGTTGGGCACTTTTGAAGA-TCATT--------------
TP53 CCGCGCCGT-GGCCATCTACAAGCAGTCACAGCACA---------
BRCA1 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT
* * * * * * *

clustalw.dnd

(
EFGR:0.41345,
BRCA1:0.43417,
TP53:0.35857);

SUMMARY:
In comparison to EGFR, BRCA1 and TP53 exhibit greater identity and resemblance with fewer
gaps, suggesting a stronger functional link. All things considered, this research highlights the
functional and evolutionary differences between these important genes linked to cancer.
QUALITY OF ALIGNMENT:
Quality of Alignment The ratings show the gaps and variances in identity, indicating a modest
level of alignment quality. Notably, EFGR and TP53 showed distinct sequences in comparison to
BRCA1 and TP53, and their pairwise score of 22.7979 indicated some functional commonality.

FUNCTIONS AND ASSOCIAED DISEASES:

EFGR: Lung cancer is linked to EFGR, which encodes a receptor tyrosine kinase involved in
cell signaling.
BRCA1: Associated with a higher risk of ovarian and breast cancer, and involved in DNA
repair.
TP53: Often altered in a variety of malignancies, this protein suppresses tumors by controlling
the cell cycle.
EVOLUTIONARY PERSPECTIVE:
While the different sequences of EFGR suggest adaptations for specific cellular functions, the
conservation of certain regions between BRCA1 and TP53 suggests shared pathways in cancer
biology. These findings highlight the diversity of gene evolution in relation to cell signaling
mechanisms and cancer susceptibility.
PHYLOGENETIC TREE:

2#

Sequence 1: CDKN2A

Sequence 2: APOE

Sequence 3: PAX6

Sequence 4: CD40

Sequence 5: TP73

CLUSTAL 2.1 Multiple Sequence Alignments

Sequence type explicitly set to DNA

Sequence format is Pearson
Sequence 1: CDKN2A 447 bp
Sequence 2: APOE 420 bp
Sequence 3: PAX6 490 bp
Sequence 4: CD40 420 bp
Sequence 5: TP73 490 bp
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 23.3333
Sequences (1:3) Aligned. Score: 24.1611
Sequences (1:4) Aligned. Score: 16.4286
Sequences (1:5) Aligned. Score: 21.9239
Sequences (2:3) Aligned. Score: 100
Sequences (2:4) Aligned. Score: 20.7143
Sequences (2:5) Aligned. Score: 22.381
Sequences (3:4) Aligned. Score: 21.4286
Sequences (3:5) Aligned. Score: 22.8571
Sequences (4:5) Aligned. Score: 19.7619
Guide tree file created: [clustalw.dnd]

There are 4 groups

Start of Multiple Alignment

Aligning...
Group 1: Sequences: 2 Score:7980
Group 2: Delayed
Group 3: Delayed
Group 4: Delayed
Alignment Score 9362

CLUSTAL-Alignment file created [clustalw.aln]

clustalw.aln

CLUSTAL 2.1 multiple sequence alignment

APOE GGATGGGGAGATAAGA-GAAGACCAGGAGGGAGTTAAATAGGGAATGGGTTGGGGGCGGC
PAX6 GGATGGGGAGATAAGA-GAAGACCAGGAGGGAGTTAAATAGGGAATGGGTTGGGGGCGGC
CDKN2A GTTCGTTGCAACAAATTGATGAGCAATGCTTTTTTATAATGCCAACTTTGTACAAAAAAG
TP73 GCGGCCGCCCCCGGCCCTGCCCGCCGGGGACGCTGGCACCGAGGATGTCCTGCCCGTGGC
CD40 -------------------------GGGAGCTGCTGGAGTCCCCATATCCTATGGGATCT
* * *

APOE TTGG---TA----AATGTG-CTGGGATTAGGCTGTTG--CAGATAATGCAACAAGGCTTG
PAX6 TTGG---TA----AATGTG-CTGGGATTAGGCTGTTG--CAGATAATGCAACAAGGCTTG
CDKN2A TTGG---CATGATGATGGG-CAGCGCCCGAGTGGCGGAGCTGCTGCTGCTCCACGGCGCG
TP73 CCAGGTCCCCGCCGCTCAC-CAGGTACTTGCCGTCCGGGGAGAACTTGCAGAGTAAGCTG
CD40 TTGGG--AAGAGGAATGACTCAGGCATCAAGCCCC-----AAGGAATTCTGTTCTGTTCA
* * * * * *

APOE GAAGGCT--AACCTG--GGACTGGCCAATCACAGGCAGGAAGATGAAGGTTCTGT---GG
PAX6 GAAGGCT--AACCTG--GGACTGGCCAATCACAGGCAGGAAGATGAAGGTTCTGT---GG
CDKN2A GAGCCCA--ACTGCGCCGACCCCGCCACTCTCACCCGACCCGTGCACGACGCTGCCC-GG
TP73 GAGAGCTTGAATACCTCGGAGAAGTTCATGGCCGCC-GCCTGCCGCGGGCGCCACCCTGC
CD40 GAGAATAT-TGTGAGTTTACAGTACCATTGCTTTGTAAAAATACCAGAATGATTCTCTGG
** * *

APOE GCTGCGTTGCTGGTCACATTCCTGGCAGGATGCCAGGCCAAGGTGGAGCAAGCGGTGGAG
PAX6 GCTGCGTTGCTGGTCACATTCCTGGCAGGATGCCAGGCCAAGGTGGAGCAAGCGGTGGAG
CDKN2A GAGGGCTTCCTGGACACGCTGGTGGTGCTGCACCGGGCCGGGGCGCGGCTGGACGTGCG-
TP73 GCCCGAAAACCCGCGGGACCCCTGGGCGCGCAGCAGGCTGCAACAGCCGACGCCG-GCCT
CD40 GTGCGATTATAATCAGCTCAGTTGACAATTTACT----TGAAAACAAACATGCCAAATA-
* ** *

APOE ACAGAGCCGGAGCCCGAGCTGCGCCAGCAGACCGAGTGGCAGAGC--GGCCAGCGC--TG
PAX6 ACAGAGCCGGAGCCCGAGCTGCGCCAGCAGACCGAGTGGCAGAGC--GGCCAGCGC--TG
CDKN2A -CGATGCCTGGGGCCG---TCTGCCCGTGGACCTGGCTGAGGAGCTGGGCCATCGCGATG
TP73 CCGAGGCCGGAAGTCAGAAGGCGGAAGTGAACT--GCAGCCTATCAGCGCCGCCGAC-TT
CD40 -TCATGC-AGGTTCCACTTTCTGTT--TTGACTT-GCACTTCAGTT-TGCAGCCTCTGTC
** * * * ** * * ** * *

APOE GGAACTGGCACTGGGTCGCTTTTGGGATTACCTGCGCTGGG---TGCAGACACTGTCTGA
PAX6 GGAACTGGCACTGGGTCGCTTTTGGGATTACCTGCGCTGGG---TGCAGACACTGTCTGA
CDKN2A TCGCACGGTACCTGCGCGCGGCTGCGGGGGGCACCAGAGGC---AGTAACCA-TGCCCGC
TP73 CCGCGCGGCATTGTGGGGCTTGTAGTTCTTGTGCCGCAGGGCTTTAAAGGAAACGCCCAC
CD40 CTGGATGACTTTTACCTTTCTGCTGAAGAAGTTGCAACGGAGATTTCAAGATCCCTTCAA
* * ** *

APOE GCAGGTGCAGGAGGAGCTGC-TCAGC--TCCCAGGTCACCCAGGAACTGAGGGCGCTGAT
PAX6 GCAGGTGCAGGAGGAGCTGC-TCAGC--TCCCAGGTCACCCAGGAACTGAGGGCGCTGAT
CDKN2A ATAGATGCCGCGGAAGGTCCCTCAGACATCCCCGATAGCCCAACTTTCTTGTACAAAGTT
TP73 GTTTCTTCCGACCAGGGATTTCCGACCCGAGAACCTTACCTCAAAGGCCGGGAGGCCTTT
CD40 ATTGC--ACAATTCTGTTTTTAGGTCCATCCAGAACCACCCACTGCATGCAGAGAAAAAC
* **

APOE GGACGAGACCATGAAGGAGTTGAAGGCC--------------------------------
PAX6 GGACGAGACCATGAAGGAGTTGAAGGCCTACAAATCGGAACTGGAGGAACAACTGACCCC
CDKN2A GGC--ATTATAAGAAAGCATTGCTTATCAATTTGTTGCAACGAAC---------------
TP73 GAGC-ACCTCCAGCTAGGGCTGCTGATAAAAATGTAGAAAGCACAGTAAAATTTGAATTT
CD40 AGTACCTAATAAACAGTCAGTGCTGTTCTTTGTGCCAGCCAGGTGA--------------
**

APOE --------------------------------------
PAX6 GGTGGCGGAGGAGACGCGGGCACGGCTGTCCAAGGAGC
CDKN2A --------------------------------------
TP73 CAGATTCACAACAAATC---------------------
CD40 --------------------------------------

clustalw.dnd
(
(
CDKN2A:0.39461,
(
APOE:0.00336,
PAX6:-0.00336)
:0.36792)
:0.01244,
CD40:0.41880,
TP73:0.38358);

SUMMARY:

This multiple sequence alignment of CDKN2A, APOE, PAX6, CD40, and TP73 reveals high
similarity between APOE and PAX6, indicating potential functional overlap, while CDKN2A
shows distinct characteristics relevant to tumor suppression.

ALIGNMENT QUALITY: The alignment quality is good, with varying scores reflecting
differences in identity and gaps; CDKN2A had a lower alignment score compared to APOE and
PAX6, which had the highest score of 100.

FUNCTIONS AND ASSOCIAED DISEASES:

1. CDKN2A: Tumor suppressor gene associated with melanoma risk.

2. APOE: Involved in lipid metabolism, associated with Alzheimer's disease.
3. PAX6: Crucial for eye development; mutations can lead to congenital eye disorders.
4. CD40: Plays a role in immune response; linked to various autoimmune diseases.
5. TP73: Regulates the cell cycle and apoptosis; associated with tumor suppression.

EVOLUTIONARY PERSPECTIVE:

From an evolutionary perspective, the conserved regions highlight functional relationships,

suggesting that while some genes share common pathways (like APOE and PAX6), others, like
CDKN2A, have diverged to fulfill specialized roles in cancer biology.
PHYLOGENETIC TREE: