MTH60-202 Molecular Biology

Wk.3: Introduction to Bioinformatics

Student guide
 1. Nucleotide BLAST

>Q1
ATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT
TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCT
TGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAA
1. Nucleotide BLAST (nucleotide -> nucleotide)
1. Nucleotide BLAST (nucleotide -> nucleotide)
Nucleotide BLAST (nucleotide -> nucleotide)
 2. BLASTx (translated nucleotide -> protein)

>Q2
ATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT
TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCT
TGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAA
2. BLASTx (translated nucleotide -> protein)
2. BLASTx (translated nucleotide -> protein)
2. BLASTx (translated nucleotide -> protein)
 3. Protein BLAST (protein -> protein)

>Q3
mysfvseetgtlivnsvllflafvvvllvtlailtalrlcayccnivnvslvkpsfyvysrvknlnssrvpdllv
3. Protein BLAST (protein -> protein)
3. Protein BLAST (protein -> protein)
3. Protein BLAST (protein -> protein)
 4. tblastn (protein -> translated nucleotide)

>Q4
mysfvseetgtlivnsvllflafvvvllvtlailtalrlcayccnivnvslvkpsfyvysrvknlnssrvpdllv
4. tblastn (protein -> translated nucleotide)
4. tblastn (protein -> translated nucleotide)
4. tblastn (protein -> translated nucleotide)
 4. tblastn (protein -> translated nucleotide)

ORIGIN
1 atgtactcat tcgtttcgga agagacaggt acgttaatag ttaatagcgt acttcttttt
61 cttgctttcg cggtattctt gctagttaca ctagccatcc ttactgcgct tcgattgtgt
121 gcgtactgct gcaatattgt taacgtgagt cttgtaaaac cttcttttta cgtttactct
181 cgtgttaaaa atctgaattc ttctagagtt cctgatcttc tggtctaa
 5. Multiple Sequence Alignment-COBALT

> [Homo sapiens]

MAAAAGMLLLGLLQAGGSVLGQAMEKVTGGNLLSMLLIACAFTLSLVYLIRLAAGHLVQLPAGVKSPPYIFSPIPFLGHAIAFGKS
PIEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEDVYSRLTTPVFGKGVAYDVPNPVFLEQKKMLKSGLNIA
HFKQHVSIIEKETKEYFESWGESGEKNVFEALSELIILTASHCLHGKEIRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRR
DRAHREIKDIFYKAIQKRRQSQEKIDDILQTLLDATYKDGRPLTDDEVAGMLIGLLLAGQHTSSTTSAWMGFFLARDKTLQKKCYL
EQKTVCGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIMMRMARTPQTVAGYTIPPGHQVCVSPTVNQRLKDSWVERLDFN
PDRYLQDNPASGEKFAYVPFGAGRHRCIGENFAYVQIKTIWSTMLRLYEFDLIDGYFPTVNYTTMIHTPENPVIRYKRRSK
 5. Multiple Sequence Alignment-COBALT

> [Pan troglodytes]

MAAAAGMLPLGLLQAGGSVLGQAMEKVTGGNLLSMLLIACAFTLSLVYLFRLAAGHLVQLPAGVKSPPYIFSPIPFL
GHAIAFGKSPIEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEDVYSRLTTPVFGKGVAYDVP
NPVFLEQKKMLKSGLNIAHFKQHVSIIEKETKEYFQSWGESGEKNVFEALSELIILTASHCLHGKEIRSQLNEKVAQLY
ADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKDIFYKAIQKRRQSQEKIDDILQTLLDATYKDGRPLTDDEVAG
MLIGLLLAGQHTSSTTSAWMGFFLARDKTLQEKCYLEQKTVCGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIM
MRMARTPQTVAGYTIPPGHQVCVSPTVNQRLKDSWVERLDFNPDRYLQDNPASGEKFAYVPFGAGRHRCIGEN
FAYVQIKTIWSTMLRLYEFDLIDGYFPTVNYTTMIHTPENPVIRYKRRSK

> [Canis lupus familiaris]

MLLLGLLQAGGSVLGQAMERVTGGNLLSMLLIACAFTLGLVYLIRLAVGHLAPLPAGAKSPPYIFSPIPFLGHAIAFG
KSPIEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEDVYSRLTTPVFGKGVAYDVPNPVFLEQK
KMLKSGLNIAHFRQHVSIIEKETKEYFQSWGESGEKNLFEALSELIILTASHCLHGKEIRSQLNEKVAQLYADLDGGFS
HAAWLLPGWLPLPSFRRRDRAHREIKNIFYKAIQKRRQSEEKIDDILQTLLDSTYKDGRPLTDDEVAGMLIGLLLAG
QHTSSTTSAWMGFFLARDKTLQDKCYLEQKTVCGEDLPPLTYDQLKDLNLLDRCIKETLRLRPPIMTMMRMAKTP
QTIAGYTIPPGHQVCVSPTVNQRLKDSWVERLDFNPDRYLQDNPASGEKFAYVPFGAGRHRCIGENFAYVQIKTIW
STMLRLYEFDLIDGYFPTVNYTTMIHTPENPVIRYKRRSK
 5. Multiple Sequence Alignment-COBALT

> [Mus musculus]

MVLLGLLQSGGWVLGQAMEQVTGGNLLSTLLIACAFTLSLVYLFRLAVGHMVQLPAGAKSPPHIYSPIPFLGHAIAF
GKSPIEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEEVYGRLTTPVFGKGVAYDVPNAIFLEQ
KKIIKSGLNIAHFKQYVPIIEKEAKEYFQSWGESGERNVFEALSELIILTASHCLHGKEIRSQLNEKVAQLYADLDGGFT
HAAWLLPAWLPLPSFRRRDRAHREIKNIFYKAIQKRRLSKEPAEDILQTLLDSTYKDGRPLTDEEISGMLIGLLLAGQH
TSSTTSAWMGFFLAKDKPLQEKCYLEQKAVCGEDLPPLTYDQLKDLNLLDRCIKETLRLRPPIMTMMRMAKTPQT
VAGYTIPPGHQVCVSPTVNQRLKDSWAERLDFNPDRYLQDNPASGEKFAYVPFGAGRHRCVGENFAYVQIKTIWS
TMLRLYEFDLINGYFPTVNYTTMIHTPENPVIRYKRRSK

> [Saccharomyces cerevisiae S288C]

MSATKSIVGEALEYVNIGLSHFLALPLAQRISLIIIIPFIYNIVWQLLYSLRKDRPPLVFYWIPWVGSAVVYGMKPYEFF
EECQKKYGDIFSFVLLGRVMTVYLGPKGHEFVFNAKLADVSAEAAYAHLTTPVFGKGVIYDCPNSRLMEQKKFVKG
ALTKEAFKSYVPLIAEEVYKYFRDSKNFRLNERTTGTIDVMVTQPEMTIFTASRSLLGKEMRAKLDTDFAYLYSDLDK
GFTPINFVFPNLPLEHYRKRDHAQKAISGTYMSLIKERRKNNDIQDRDLIDSLMKNSTYKDGVKMTDQEIANLLIGV
LMGGQHTSAATSAWILLHLAERPDVQQELYEEQMRVLDGGKKELTYDLLQEMPLLNQTIKETLRMHHPLHSLFRK
VMKDMHVPNTSYVIPAGYHVLVSPGYTHLRDEYFPNAHQFNIHRWNKDSASSYSVGEEVDYGFGAISKGVSSPYL
PFGGGRHRCIGEHFAYCQLGVLMSIFIRTLKWHYPEGKTVPPPDFTSMVTLPTGPAKIIWEKRNPEQKI
5. Multiple Sequence Alignment-COBALT

ใส่ Sequence ของ Homo sapiens

จากสไลด์ท่ี 19
20 ลงในช่องนี ้

ใส่ Sequence ทีเ่ หลือ

จากสไลด์ที่ 20 - 21 ลงในช่องนี้
21-22
5. Multiple Sequence Alignment-COBALT
5. Multiple Sequence Alignment-COBALT
6. Phylogenetic tree
6. Phylogenetic tree

A
Have a nice day