1. Alignment Sequence, Structure, Network
Jong Bhak

2. Alignment is the key in bioinformatics
Alignment is the best method in comparing things in the whole universe
The universe is a gigantic sequence

3. Amino Acids Representation
Ala alanine Met methionine Asp aspartate Phe phenylalanine Arg arginine Pro proline Asn asparagine Ser serine Cys cysteine Thr threonine Glu glutamate Trp tryptophan Gln glutamine Tyr tyrosine Gly glycine Val valine Glx glutamate or glutamine *** any His histidine --- gap of indeterminate length Ileu isoleucine TGA translation stop Lys lysine TAG translation stop Leu leucine TAA translation stop

4. Single Sequence representations
There are several commonly used pure sequence representation formats in “flat files”
FASTA (most commonly used for raw sequence data)
PIR
Representations in Databases (such as MySQL)
As columns and rows
Representations in programs or objects
@codons = $myCodonTable->revtranslate('A');
Flat file FASTA format 
> gi|532319|pir|TVFV2E|TVFV2E envelope protein
CCTCTCGGAGCTGGAAATGCAGCTATTGAGATCTTCGAATGCTGC
AGCTGGAGGCGGAGGCAGCTGGGGAGGTCCGAGCGATGTGACC
GGCCGCCATCGCTCGTCTCTTCCTCTCTCCTGCCGCCTCCTGTGT
CGAAAATAACTTTTTTAGTCTAAAGAAAGAAAG
>gi|532319|pir|TVFV2E|TVFV2E envelope protein
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTLLL
SYSENRTAPTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXX

5. Accessing Bioperl CodonTable (from object oriented module)
use Bio::Tools::CodonTable;
# defaults to ID 1 "Standard"
$myCodonTable = Bio::Tools::CodonTable->new();
$myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 3 );
# change codon table
$myCodonTable->id(5);
# examine codon table
print join (' ', "The name of the codon table no.", $myCodonTable->id(4),
"is:", $myCodonTable->name(), "\n");
# translate a codon
$aa = $myCodonTable->translate('ACU');
$aa = $myCodonTable->translate('act');
$aa = $myCodonTable->translate('ytr');
# reverse translate an amino acid
@codons = $myCodonTable->revtranslate('A');
@codons = $myCodonTable->revtranslate('Ser');
@codons = $myCodonTable->revtranslate('Glx');
@codons = $myCodonTable->revtranslate('cYS', 'rna');

6. FASTA (flat file)
Sequences are expected to be represented in the standard
IUB/IUPAC amino acid and nucleic acid codes
* International Union of Pure and Applied Chemistry
Lower-case letters are accepted
A single hyphen or dash can be used to represent a gap of indeterminate length
In amino acid sequences, U and * are acceptable letters
Numerical digits in the query sequence should either be removed or replaced by appropriate letter codes (e.g., N for unknown
nucleic acid residue or X for unknown amino acid residue

7. Nucleic Acids’ FASTA A --> adenosine M --> A C (amino)
C --> cytidine S --> G C (strong)
G --> guanine W --> A T (weak)
T --> thymidine B --> G T C
U --> uridine D --> G A T
R --> G A (purine) H --> A C T
Y --> T C (pyrimidine) V --> G C A
K --> G T (keto) N --> A G C T (any)
X --> for unknown gap of indeterminate length

8. Protein sequences in FASTA
A alanine P proline
B aspartate or asparagine Q glutamine
C cystine R arginine
D aspartate S serine
E glutamate T threonine
F phenylalanine U selenocysteine
G glycine V valine
H histidine W tryptophan
I isoleucine Y tyrosine
K lysine Z glutamate or glutamine
L leucine X any
M methionine * translation stop
N asparagine gap of indeterminate length

9. PIR (NBRF) sequence format
>P1;CRAB_ANAPL ALPHA CRYSTALLIN B CHAIN (ALPHA (BCRYSTALLIN). MDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELLPASP LSPFLMRSPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKVKVLGDMVEIHGKHEERQDEHGFIAREFNR KYRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIP TREEKPAIAG AQRK*

10. PIR format
A sequence in PIR format consists of: 1.One line starting with a. a ">" (greater-than) sign, followed by b. a two-letter code describing the sequence type (P1, F1, DL, DC, RL, RC, or XX), followed by c. a semicolon, followed by d. the sequence identification code (the database ID-code). 2. One line containing a textual description of the sequence. 3. One or more lines containing the sequence itself. The end of the sequence is marked by a "*" (asterisk) character. A file in PIR format may comprise more than one sequence. The PIR format is also often referred to as the NBRF format.

11. GenBank style (flat file)
LOCUS ABCAARAA_1
DEFINITION A.aceti acetic acid resistance protein (aarA) gene, complete cds;
acetic acid resistance protein (aarA).
DATE SEP-1990
ACCESSION M34830
ORGANISM Acetobacter aceti
Eubacteria; Proteobacteria; alpha subdivision; Acetobacteraceae;
Acetobacter.
COMMENT CDS
/db_xref="PID:g141730"
WEIGHT
LENGTH
ORIGIN Translated using phase 1
1 MSASQKEGKL STATISVDGK SAEMPVLSGT LGPDVIDIRK LPAQLGVFTF DPGYGETAAC
61 NSKITFIDGD KGVLLHRGYP IAQLDENASY EEVIYLLLNG ELPNKVQYDT FTNTLTNHTL
121 LHEQIRNFFN GFRRDAHPMA ILCGTVGALS AFYPDANDIA IPANRDLAAM RLIAKIPTIA
181 AWAYKYTQGE AFIYPRNDLN YAENFLSMMF ARMSEPYKVN PVLARAMNRI LILHADHEQN
241 ASTSTVRLAG STGANPFACI AAGIAALWGP AHGGANEAVL KMLARIGKKE NIPAFIAQVK
301 DKNSGVKLMG FGHRVYKNFD PRAKIMQQTC HEVLTELGIK DDPLLDLAVE LEKIALSDDY
361 FVQRKLYPNV DFYSGIILKA MGIPTSMFTV LFAVARTTGW VSQWKEMIEE PGQRISRPRQ
421 LYIGAPQRDY VPLAKR //

12. EMBL style ID CM23SRIBR converted; DNA; UNC; 805 BP. XX AC X80636;
DT 22-MAR-1995
DE C.mucosalis gene for 23S ribosomal RNA (fragment)
OS Campylobacter mucosalis
CC SEQIO retrieval from EMBL-format entry Feb-1996
SQ Sequence 805 BP; 226 A; 158 C; 224 G; 194 T; 3 other;
gattctgcgc ggaaaatata acggggctaa aatgagtacc gaagctttag acttagtttt
actaagtggt aggagcgttc tattcagcgt tgaaggtgta ccggtaagga gcgctggagc
ggatagaagt gagcatgcag gcatgagtag cgataattgg ggtgagaatc cccaacgccg
taarcccaag gtttcctacg cgatgctcgt catcgtaggg ttagccgggt cctaagcaaa
gtccgaaagg ggtatgcgat ggaaaattgg ttaatattcc aatgccaaca ttattgtgcg
atggaaggac gcttagagtt aaaggagcca gctgatggaa gtgctggtcg aaaggtgtag
gttgagttac aggcaaatcc gtaactcttt atccgagacc ccacaggcgt ttgaagttct
tcggaatgga tgacgaatcc ttgatactgt cgagccaaga aaagtttcta agtttagata
atgttgcccg taccgtaaac cgacacaggt gggtgggatg agtattctaa ggcgcgtgga
agaactctct tcaaggaact ctgcaaaata gcaccgtatc ttcggtataa ggtgtgccta
actttgtgaa ggatttactc cgtaagcatt gaaggttaca acaaagagtc cctcccgact
gtttaccaaa aacacagcac tctgctaact cgtaagagga tgtatagggt gtgacgcctg
cccggtgctc gaaggttaat tgatggggty agcagyaatg cgaagctctt gatcgaagcc
cgagtaaacg gccgccgtaa ctata //

13. Swissprot style ID 104K_THEPA CONVERTED; PRT; 924 AA. AC P15711;
DT 01-AUG-1992
DE KD MICRONEME-RHOPTRY ANTIGEN.
OS THEILERIA PARVA.
CC -!- DEVELOPMENTAL STAGE: SPOROZOITE ANTIGEN.
CC -!- SUBCELLULAR LOCATION: IN MICRONEME/RHOPTRY COMPLEXES. CC
CC SEQIO retrieval from Swiss-Prot database entry Feb-1996
SQ SEQUENCE AA;
MKFLILLFNI LCLFPVLAAD NHGVGPQGAS GVDPITFDIN SNQTGPAFLT AVEMAGVKYL
QVQHGSNVNI HRLVEGNVVI WENASTPLYT GAIVTNNDGP YMAYVEVLGD PNLQFFIKSG
DAWVTLSEHE YLAKLQEIRQ AVHIESVFSL NMAFQLENNK YEVETHAKNG ANMVTFIPRN
GHICKMVYHK NVRIYKATGN DTVTSVVGFF RGLRLLLINV FSIDDNGMMS NRYFQHVDDK
YVPISQKNYE TGIVKLKDYK HAYHPVDLDI KDIDYTMFHL ADATYHEPCF KIIPNTGFCI
TKLFDGDQVL YESFNPLIHC INEVHIYDRN NGSIICLHLN YSPPSYKAYL VLKDTGWEAT
THPLLEEKIE ELQDQRACEL DVNFISDKDL YVAALTNADL NYTMVTPRPH RDVIRVSDGS
EVLWYYEGLD NFLVCAWIYV SDGVASLVHL RIKDRIPANN DIYVLKGDLY WTRITKIQFT
QEIKRLVKKS KKKLAPITEE DSDKHDEPPE GPGASGLPPK APGDKEGSEG HKGPSKGSDS
SKEGKKPGSG KKPGPAREHK PSKIPTLSKK PSGPKDPKHP RDPKEPRKSK SPRTASPTRR
PSPKLPQLSK LPKSTSPRSP PPPTRPSSPE RPEGTKIIKT SKPPSPKPPF DPSFKEKFYD
DYSKAASRSK ETKTTVVLDE SFESILKETL PETPGTPFTT PRPVPPKRPR TPESPFEPPK
DPDSPSTSPS EFFTPPESKR TRFHETPADT PLPDVTAELF KEPDVTAETK SPDEAMKRPR
SPSEYEDTSP GDYPSLPMKR HRLERLRLTT TEMETDPGRM AKDASGKPVK LKRSKSFDDL
TTVELAPEPK ASRIVVDDEG TEADDEETHP PEERQKTEVR RRRPPKKPSK SPRPSKPKKP
KKPDSAYIPS ILAILVVSLI VGIL //

14. Sequence profile/model representations
Models : Hidden Markov Models
Profiles : A propensity mapping of multiple sequences.

15. Alignment
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAA

16. AAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAA
AAAAAAAGGGGGGGAAAAAAAAAAAAAAAAAAAAA AAAA

17. Gapped alignment AAAAAA_____ATAAAAAAAAAAAAAAAAAAAAAA AAAA
AAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAA
AAAAAAATAAAAAAAAAAA___AAAAAAAAAAAAA GAAA
AAAA__AGGGGG____AAAAAAAAAAA_____AAA AAAA

18. Sequence identity?

19. Sequence Homology?

20. Genetic Distance?

21. Distance matrix

22. Exchange matrix
A->G ?
A->T ?
K->M ?

23. HMM