Bioinfo-Assignment-1

I. Assembly and de Bruijn graph. Given the following reads, draw the de Bruijn graph (3-mer as node), and write down what is the whole sequence.

De Bruijin

Path:

ATGCTAG
ATGCTGACTAG

2. Here is the position and weight of all exon segments in an abstract sequence of length 18. Please find a maximum set of non-overlapping putative exons based on brute force or dynamic programming.

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18
0	0	5	5	5	5	5	16	16	16	16	16	16	19	22	22	22	24

Selected exons:

left	right	weight
2	3	5
4	8	11
9	10	0
11	15	6
16	18	2

3. Please generate a dynamic programming matrix for sequence alignment and find its optimum alignment score.

$S e q u e n c e_{A}$ : $G A T C A G A T C G A$ $S e q u e n c e_{B}$ : $G G T A A C G T$ $S c o r i n g s y s t e m$ : $+ 5$ for a match; $- 2$ for a mismatch; $- 6$ for each indel

		G	A	T	C	A	G	A	T	C	G	A
		-6	-12	-18	-24	-30	-36	-42	-48	-54	-60	-66
G	-6		-1	-7	-13	-19	-25	-31	-37	-43	-49	-55
G	-12	-1		-3	-9	-15	-14	-20	-26	-32	-38	-44
T	-18	-7	-3		2	-4	-10	-16	-15	-21	-27	-33
A	-24	-13	-2	2			1	-5	-11	-17	-23	-22
A	-30	-19	-8	-4	0				0	-6	-12	-18
C	-36	-25	-14	-10	1	5	9	3			-1	-7
G	-42	-31	-20	-16	-5	-1	10	7	1	2		4
T	-48	-37	-26	-15	-11	-7	4	8	12	6	4

$S e q u e n c e_{A}$ : GATC_AGATCGA $S e q u e n c e_{B}$ : GGT_AA_A_CGT

4. To apply database/resource and tools

Search genes associated with colon cancer in human genome.

1. Give the DNA sequence of MLH1 (nucleotide NM_000249).

DNA Sequence of MLH1*

fasta

>NM_000249.4 Homo sapiens mutL homolog 1 (MLH1), transcript variant 1, mRNA
AGACGTTTCCTTGGCTCTTCTGGCGCCAAAATGTCGTTCGTGGCAGGGGTTATTCGGCGGCTGGACGAGA
CAGTGGTGAACCGCATCGCGGCGGGGGAAGTTATCCAGCGGCCAGCTAATGCTATCAAAGAGATGATTGA
GAACTGTTTAGATGCAAAATCCACAAGTATTCAAGTGATTGTTAAAGAGGGAGGCCTGAAGTTGATTCAG
ATCCAAGACAATGGCACCGGGATCAGGAAAGAAGATCTGGATATTGTATGTGAAAGGTTCACTACTAGTA
AACTGCAGTCCTTTGAGGATTTAGCCAGTATTTCTACCTATGGCTTTCGAGGTGAGGCTTTGGCCAGCAT
AAGCCATGTGGCTCATGTTACTATTACAACGAAAACAGCTGATGGAAAGTGTGCATACAGAGCAAGTTAC
TCAGATGGAAAACTGAAAGCCCCTCCTAAACCATGTGCTGGCAATCAAGGGACCCAGATCACGGTGGAGG
ACCTTTTTTACAACATAGCCACGAGGAGAAAAGCTTTAAAAAATCCAAGTGAAGAATATGGGAAAATTTT
GGAAGTTGTTGGCAGGTATTCAGTACACAATGCAGGCATTAGTTTCTCAGTTAAAAAACAAGGAGAGACA
GTAGCTGATGTTAGGACACTACCCAATGCCTCAACCGTGGACAATATTCGCTCCATCTTTGGAAATGCTG
TTAGTCGAGAACTGATAGAAATTGGATGTGAGGATAAAACCCTAGCCTTCAAAATGAATGGTTACATATC
CAATGCAAACTACTCAGTGAAGAAGTGCATCTTCTTACTCTTCATCAACCATCGTCTGGTAGAATCAACT
TCCTTGAGAAAAGCCATAGAAACAGTGTATGCAGCCTATTTGCCCAAAAACACACACCCATTCCTGTACC
TCAGTTTAGAAATCAGTCCCCAGAATGTGGATGTTAATGTGCACCCCACAAAGCATGAAGTTCACTTCCT
GCACGAGGAGAGCATCCTGGAGCGGGTGCAGCAGCACATCGAGAGCAAGCTCCTGGGCTCCAATTCCTCC
AGGATGTACTTCACCCAGACTTTGCTACCAGGACTTGCTGGCCCCTCTGGGGAGATGGTTAAATCCACAA
CAAGTCTGACCTCGTCTTCTACTTCTGGAAGTAGTGATAAGGTCTATGCCCACCAGATGGTTCGTACAGA
TTCCCGGGAACAGAAGCTTGATGCATTTCTGCAGCCTCTGAGCAAACCCCTGTCCAGTCAGCCCCAGGCC
ATTGTCACAGAGGATAAGACAGATATTTCTAGTGGCAGGGCTAGGCAGCAAGATGAGGAGATGCTTGAAC
TCCCAGCCCCTGCTGAAGTGGCTGCCAAAAATCAGAGCTTGGAGGGGGATACAACAAAGGGGACTTCAGA
AATGTCAGAGAAGAGAGGACCTACTTCCAGCAACCCCAGAAAGAGACATCGGGAAGATTCTGATGTGGAA
ATGGTGGAAGATGATTCCCGAAAGGAAATGACTGCAGCTTGTACCCCCCGGAGAAGGATCATTAACCTCA
CTAGTGTTTTGAGTCTCCAGGAAGAAATTAATGAGCAGGGACATGAGGTTCTCCGGGAGATGTTGCATAA
CCACTCCTTCGTGGGCTGTGTGAATCCTCAGTGGGCCTTGGCACAGCATCAAACCAAGTTATACCTTCTC
AACACCACCAAGCTTAGTGAAGAACTGTTCTACCAGATACTCATTTATGATTTTGCCAATTTTGGTGTTC
TCAGGTTATCGGAGCCAGCACCGCTCTTTGACCTTGCCATGCTTGCCTTAGATAGTCCAGAGAGTGGCTG
GACAGAGGAAGATGGTCCCAAAGAAGGACTTGCTGAATACATTGTTGAGTTTCTGAAGAAGAAGGCTGAG
ATGCTTGCAGACTATTTCTCTTTGGAAATTGATGAGGAAGGGAACCTGATTGGATTACCCCTTCTGATTG
ACAACTATGTGCCCCCTTTGGAGGGACTGCCTATCTTCATTCTTCGACTAGCCACTGAGGTGAATTGGGA
CGAAGAAAAGGAATGTTTTGAAAGCCTCAGTAAAGAATGCGCTATGTTCTATTCCATCCGGAAGCAGTAC
ATATCTGAGGAGTCGACCCTCTCAGGCCAGCAGAGTGAAGTGCCTGGCTCCATTCCAAACTCCTGGAAGT
GGACTGTGGAACACATTGTCTATAAAGCCTTGCGCTCACACATTCTGCCTCCTAAACATTTCACAGAAGA
TGGAAATATCCTGCAGCTTGCTAACCTGCCTGATCTATACAAAGTCTTTGAGAGGTGTTAAATATGGTTA
TTTATGCACTGTGGGATGTGTTCTTCTTTCTCTGTATTCCGATACAAAGTGTTGTATCAAAGTGTGATAT
ACAAAGTGTACCAACATAAGTGTTGGTAGCACTTAAGACTTATACTTGCCTTCTGATAGTATTCCTTTAT
ACACAGTGGATTGATTATAAATAAATAGATGTGTCTTAACATAA

2. Give the DNA sequence of E. coli mismatch repair gene mutS.

DNA Sequence of E. coli mismatch repair gene mutS

fasta

>NC_000913.3:2857093-2859654 Escherichia coli str. K-12 substr. MG1655, complete genome
ATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTATCTCAGGCTGAAAGCCCAGC
ATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGC
GTCGCAACTGCTGGATATTTCACTGACCAAACGCGGTGCTTCGGCGGGAGAGCCGATCCCGATGGCGGGG
ATTCCCTACCATGCGGTGGAAAACTATCTCGCCAAACTGGTGAATCAGGGAGAGTCCGTTGCCATCTGCG
AACAAATTGGCGATCCGGCGACCAGCAAAGGTCCGGTTGAGCGCAAAGTTGTGCGTATCGTTACGCCAGG
CACCATCAGCGATGAAGCCCTGTTGCAGGAGCGTCAGGACAACCTGCTGGCGGCTATCTGGCAGGACAGC
AAAGGTTTCGGCTACGCGACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCG
AAACGATGGCGGCAGAACTGCAACGCACTAATCCTGCGGAACTGCTGTATGCAGAAGATTTTGCTGAAAT
GTCGTTAATTGAAGGCCGTCGCGGCCTGCGCCGTCGCCCGCTGTGGGAGTTTGAAATCGACACCGCGCGC
CAGCAGTTGAATCTGCAATTTGGGACCCGCGATCTGGTCGGTTTTGGCGTCGAGAACGCGCCGCGCGGAC
TTTGTGCTGCCGGTTGTCTGTTGCAGTATGCGAAAGATACCCAACGTACGACTCTGCCGCATATTCGTTC
CATCACCATGGAACGTGAGCAGGACAGCATCATTATGGATGCCGCGACGCGTCGTAATCTGGAAATCACC
CAGAACCTGGCGGGTGGTGCGGAAAATACGCTGGCTTCTGTGCTCGACTGCACCGTCACGCCGATGGGCA
GCCGTATGCTGAAACGCTGGCTGCATATGCCAGTGCGCGATACCCGCGTGTTGCTTGAGCGCCAGCAAAC
TATTGGCGCATTGCAGGATTTCACCGCCGGGCTACAGCCGGTACTGCGTCAGGTCGGCGACCTGGAACGT
ATTCTGGCACGTCTGGCTTTACGAACTGCTCGCCCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGC
AACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGAT
GGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCAATCATCGACACACCGCCGGTGCTGGTACGC
GACGGTGGTGTTATCGCATCGGGCTATAACGAAGAGCTGGATGAGTGGCGCGCGCTGGCTGACGGCGCGA
CCGATTATCTGGAGCGTCTGGAAGTCCGCGAGCGTGAACGTACCGGCCTGGACACGCTGAAAGTTGGCTT
TAATGCGGTGCACGGCTACTACATTCAAATCAGCCGTGGGCAAAGCCATCTGGCACCCATCAACTACATG
CGTCGCCAGACGCTGAAAAACGCCGAGCGCTACATCATTCCAGAGCTAAAAGAGTACGAAGATAAAGTTC
TCACCTCAAAAGGCAAAGCACTGGCACTGGAAAAACAGCTTTATGAAGAGCTGTTCGACCTGCTGTTGCC
GCATCTGGAAGCGTTGCAACAGAGCGCGAGCGCGCTGGCGGAACTCGACGTGCTGGTTAACCTGGCGGAA
CGGGCCTATACCCTGAACTACACCTGCCCGACCTTCATTGATAAACCGGGCATTCGCATTACCGAAGGTC
GCCATCCGGTAGTTGAACAAGTACTGAATGAGCCATTTATCGCCAACCCGCTGAATCTGTCGCCGCAGCG
CCGCATGTTGATCATCACCGGTCCGAACATGGGCGGTAAAAGTACCTATATGCGCCAGACCGCACTGATT
GCGCTGATGGCCTACATCGGCAGCTATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCT
TTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAAC
CGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCC
ACCTACGATGGTCTGTCGCTGGCGTGGGCGTGCGCGGAAAATCTGGCGAATAAGATTAAGGCATTGACGT
TATTTGCTACCCACTATTTCGAGCTGACCCAGTTACCGGAGAAAATGGAAGGCGTCGCTAACGTGCATCT
CGATGCACTGGAGCACGGCGACACCATTGCCTTTATGCACAGCGTGCAGGATGGCGCGGCGAGCAAAAGC
TACGGCCTGGCGGTTGCAGCTCTGGCAGGCGTGCCAAAAGAGGTTATTAAGCGCGCACGGCAAAAGCTGC
GTGAGCTGGAAAGCATTTCGCCGAACGCCGCCGCTACGCAAGTGGATGGTACGCAAATGTCTTTGCTGTC
AGTACCAGAAGAAACTTCGCCTGCGGTCGAAGCTCTGGAAAATCTTGATCCGGATTCACTCACCCCGCGT
CAGGCGCTGGAGTGGATTTATCGCTTGAAGAGCCTGGTGTAA

3. Compare MLH1 and mutS (answer of previous two questions) sequence.

Blastn

NJwzTn

4. Translate the above two gene sequences to protein sequences.

Human MLH1 Protein Sequence

txt

MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERF
TTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIA
TRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAF
KMNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE
SILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL
SKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVE
MVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELF
YQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLP
LLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIV
YKALRSHILPPKHFTEDGNILQLANLPDLYKVFERCL

MLH

E. coli mismatch repair gene mutS Protein Sequence

txt

MSAIENFDAHTPMMQQYLRLKAQHPEILLFYRMGDFYELFYDDAKRASQLLDISLTKRGASAGEPIPMAGIPYHAVENYL
AKLVNQGESVAICEQIGDPATSKGPVERKVVRIVTPGTISDEALLQERQDNLLAAIWQDSKGFGYATLDISSGRFRLSEP
ADRETMAAELQRTNPAELLYAEDFAEMSLIEGRRGLRRHPLWEFEIDTARQQLNLQFGTRDLVGFGVENAPRGLCAAGCL
LQYAKDTQRTTLPHIRSITMEREQDSIIMDAATRRNLEITQNLAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRV
LLERQQTIGALQDFTAGLQPVLRQVGDLERILARLALRTARPRDLARMRHAFQQLPELRAQLETVDSAPVQALREKMGEF
AELRDLLERAIIDTPPVLVRDGGVIASGYNEELDEWRALADGATDYLERLEVRERERTGLDTLKVGFNAVHGYYIQISRG
QSHLAPINYMRRQTLKNAERYIIPELKEYEDKVLTSKGKALALEKQLYEELFDLLLPHLEALQQSASALAELDVLVNLAE
RAYTLNYTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYV
PAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIK
ALTLFATHYFELTQLPEKMEGVANVHLDALEHGDTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIKRARQKLRELESIS
PNAAATQVDGTQMSLLSVPEETSPAVEALENLDPDSLTPRQALEWIYRLKSLV

E.coli

5. Perform protein sequence homology searching for MLH1 in GenBank. Give the 10 highest hits.

homology sequence

txt

>AAA17374.1 human homolog of E. coli mutL gene product, Swiss-Prot Accession Number P23367 [Homo sapiens]
MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERF
TTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIA
TRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSVFGNAVSRELIEIGCEDKTLAF
KMNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE
SILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL
SKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVE
MVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELF
YQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLP
LLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIV
YKALRSHILPPKHFTEDGNILQLANLPDLYKVFERC
>NP_000240.1 DNA mismatch repair protein Mlh1 isoform 1 [Homo sapiens]
MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERF
TTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIA
TRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAF
KMNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE
SILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL
SKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVE
MVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELF
YQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLP
LLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIV
YKALRSHILPPKHFTEDGNILQLANLPDLYKVFERC
>AAQ02400.1 mutL-like 1, colon cancer, nonpolyposis type 2, partial [synthetic construct]
MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERF
TTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIA
TRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAF
KMNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE
SILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL
SKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVE
MVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELF
YQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLP
LLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIV
YKALRSHILPPKHFTEDGNILQLANLPDLYKVFERCL
>AKI70020.1 MLH1, partial [synthetic construct]
MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERF
TTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIA
TRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAF
KMNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE
SILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL
SKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVE
MVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELF
YQILIYDFANFGVLRLSEPAPLFDLDMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLP
LLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIV
YKALRSHILPPKHFTEDGNILQLANLPDLYKVFERC
>BAG35497.1 unnamed protein product [Homo sapiens]
MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERF
TTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIA
TRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAF
KMNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE
SILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEVVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL
SKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVE
MVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELF
YQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLP
LLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIV
YKALRSHILPPKHFTEDGNILQLANLPDLYKVFERC
>AKI70018.1 MLH1, partial [synthetic construct]
MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERF
TTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIA
TRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAF
KMNDYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE
SILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL
SKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVE
MVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELF
YQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLP
LLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIV
YKALRSHILPPKHFTEDGNILQLANLPDLYKVFERC
>AAT44531.1 hypothetical rhabdomyosarcoma antigen MU-RMS-40.5, partial [Homo sapiens]
SFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFT
TSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIAT
RRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAFK
MNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEES
ILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPLS
KPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVEM
VEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELFY
QILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLPL
LIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIVY
KALRSHILPPKHFTEDGNILQLANLPDLYKVFERC
>AKI70017.1 MLH1, partial [synthetic construct]
MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKFTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERF
TTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIA
TRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAF
KMNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE
SILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL
SKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVE
MVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELF
YQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLP
LLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIV
YKALRSHILPPKHFTEDGNILQLANLPDLYKVFERC
>AKI70019.1 MLH1, partial [synthetic construct]
MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERF
TTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIA
TRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAF
KMNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE
SILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL
SKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKIHREDSDVE
MVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELF
YQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLP
LLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIV
YKALRSHILPPKHFTEDGNILQLANLPDLYKVFERC
>XP_001170433.1 DNA mismatch repair protein Mlh1 isoform X1 [Pan troglodytes]
MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERF
TTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIA
TRRKALKNPSEEYGKILEVVGRYSIHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAF
KMNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEE
SILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL
SKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVTAKNQSLEGDTTKGTSEMSEKRGPTSSNPRKRHREDSDVE
MVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINERGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLLNTTKLSEELF
YQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLP
LLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWTVEHIV
YKALRSHILPPKHFTEDGNILQLANLPDLYKVFERC

5. Please ﬁnish one of the following problems.

Write a program to calculate similarity between any pairs of protein sequences in the given input ﬁle “APOBEC3A.fasta”. (global alignment, gap penalty and gap extend penalty=-5). You can download scoring matrix from here According to your program, which two sequences are most similar?

python

from Bio import SeqIO

def read_fasta(file):
    sequences = []
    for record in SeqIO.parse(file, "fasta"):
        sequences.append(str(record.seq))
    return sequences
sequences = read_fasta("APOBEC3A.fasta")

def load_blosum62(file):
    blosum62 = {}
    with open(file) as f:
        lines = f.readlines()
        amino_acids = lines[0].split() 
        for line in lines[1:]:
            parts = line.split()
            row_acid = parts[0]  
            scores = list(map(int, parts[1:]))  
            blosum62[row_acid] = dict(zip(amino_acids, scores))
    return blosum62
def needleman_wunsch(seq1, seq2, gap_penalty, blosum62):
    n = len(seq1)
    m = len(seq2)
    score_matrix = [[0] * (m + 1) for _ in range(n + 1)]

    for i in range(1, n + 1):
        score_matrix[i][0] = gap_penalty * i
    for j in range(1, m + 1):
        score_matrix[0][j] = gap_penalty * j

    for i in range(1, n + 1):
        for j in range(1, m + 1):
            match = score_matrix[i-1][j-1] + blosum62[seq1[i-1]][seq2[j-1]]
            delete = score_matrix[i-1][j] + gap_penalty
            insert = score_matrix[i][j-1] + gap_penalty
            score_matrix[i][j] = max(match, delete, insert)

    return score_matrix[n][m]

Get the highest similarity

python

blosum62 = load_blosum62("BLOSUM62.txt")
gap_penalty = -5
sequences = read_fasta("APOBEC3A.fasta")
ans=(0,1)
res=-1
for i in range(len(sequences)):
    for j in range(i + 1, len(sequences)):
        score = needleman_wunsch(sequences[i], sequences[j], gap_penalty, blosum62)
        if score>res:
            res=score
            ans=(i,j)
        # print(f"Similarity between sequence {i+1} and {j+1}: {score}")

print(f"The most similar sequences are {ans[0]+1} and {ans[1]+1} with a similarity score of {res}")

Result

The most similar sequences are sequence APOBEC3A_Macaca_fascicularis and sequence APOBEC3A_Macaca_leonina with a similarity score of 1103

Algorithm

Tutorial

assignment

Assignment

As-1

As-2

Lab-1

Lab-2

Lab-3

Lab-4

GAMES101

Assignment-1

Assignment-2

Assignment-3

Assignment-4

Lab

Lecture

Peoject

CSCN

Ploidy

Bioinfo-Assignment-1 ​

I. Assembly and de Bruijn graph. Given the following reads, draw the de Bruijn graph (3-mer as node), and write down what is the whole sequence. ​

2. Here is the position and weight of all exon segments in an abstract sequence of length 18. Please find a maximum set of non-overlapping putative exons based on brute force or dynamic programming. ​

Selected exons: ​

3. Please generate a dynamic programming matrix for sequence alignment and find its optimum alignment score. ​

4. To apply database/resource and tools ​

1. Give the DNA sequence of MLH1 (nucleotide NM_000249). ​

2. Give the DNA sequence of E. coli mismatch repair gene mutS. ​

3. Compare MLH1 and mutS (answer of previous two questions) sequence. ​

4. Translate the above two gene sequences to protein sequences. ​

5. Perform protein sequence homology searching for MLH1 in GenBank. Give the 10 highest hits. ​

5. Please ﬁnish one of the following problems. ​

Get the highest similarity ​

Result ​