Introduction to ; An Evolutionary Approach: Appendices

Bernhard Haubold & Thomas Wiehe

ICB ­c 2006 Birkhäuser Verlag Nomenclature of Nucleic Acid Constituends

Chemical Base Structure Nucleoside Symbol Class

NH¾ N N adenine N N purine adenosine A

O H N N N guanine H¾ N N purine guanosine G

NH¾ H N cytosine O N pyrimidine cytidine C

O

H CH¿ N thymine O N pyrimidine thymidine T

O H N uracil O N pyrimidine uridine U

ICB ­c 2006 Birkhäuser Verlag Carbon Atoms in Ribose

O 5’ 4’ 1’

3’ 2’

ICB ­c 2006 Birkhäuser Verlag DNA & RNA

AB O O

H CH¿ H N N O N O N HO P O HO P O O O O O

O O OH

ICB ­c 2006 Birkhäuser Verlag Structure of DNA

ICB ­c 2006 Birkhäuser Verlag Ambiguity Codes for DNA

Symbol Meaning Symbol Meaning AA RGA BTGC SGC CC TT DTGA UT GG VGCA HTCA WTA KTG XTGCA MCA YTC NTGCA

ICB ­c 2006 Birkhäuser Verlag Amino Acid Nomenclature

One Three Name One Three Name A Ala alanine M Met methionine C Cys cysteine N Asn asparagine D Asp aspartic acid P Pro proline E Glu glutamic acid Q Gln glutamine F Phe phenylalanine R Arg arginine G Gly glycine S Ser serine H His histidine T Thr threonine I Ile isoleucine V Val valine K Lys lysine W Trp tryptophan L Leu leucine Y Tyr tyrosine

ICB ­c 2006 Birkhäuser Verlag Physico-Chemical Properties of Amino Acids

H H H

H¾ N COOH COOH

H¾ N COOH

H¾ N COOH

CH¿

CH¾ CHOH H N Ala CONH¾

CH¿ H Asn Thr Pro

H¾ N COOH H H Gly

H¾ N COOH

H CH¾ OH H H ¾ H N COOH H¾ N COOH

Ser H¾ N COOH

CH¾ CH

CH¾ SH ¿ H C CH¿ COOH Cys Asp tiny Val

small

H H H H H¾ N COOH

H¾ N COOH H

H¾ N COOH CH

H¾ N COOH ¿

H C CH¾ ¾ CH H¾ N COOH

CH¾

CH¾

CH¿

CH¾ H N Ile N Phe N His OH H Trp H H Tyr aromatic

H¾ N COOH

H¾ N COOH H

CH¾

CH¾

H¾ N COOH CH ¿ H C CH¿

CH¾

CH¾ COOH Leu CH¾

Glu CH¾ ¾ CH¾ NH H aliphatic

Lys H¾ N COOH H

CH¾

H¾ N COOH H

CH¾ ¾ CH¾ H N COOH

CONH¾ ¾ H¾ CH

C Gln ¾ CH¾ CH NH S

C CH¿

H¾ N NH Met Arg negative positive polar non−polar

ICB ­c 2006 Birkhäuser Verlag

Synthesis of Peptide Bond

Ê ¾ O

H¾ N

Ê ½

Ê O ½ OH O N

H¾ N OH

H¾ N

Ê

¾ C OH Æ O

ICB ­c 2006 Birkhäuser Verlag Standard Genetic Code

second position 5’ end 3’ end T C A G T Phe/F Tyr/Y Cys/C Ser/S C Ter/* A Ter/* T Trp/W G Leu/L T His/H Pro/P Arg/R C A Gln/Q C G T Asn/N Ser/S Ile/I Thr/T C A Lys/K Arg/R A Met/M G T Asp/D Val/V Ala/A Gly/G C A Glu/E G G

ICB ­c 2006 Birkhäuser Verlag Applications

Program Purpose Reference Website BLAST Databasesearch [2] www.ncbi.nlm.nih.gov/BLAST clustalw Multiple [12] ftp-igbmc.u-strasbg.fr/pub EMBOSS Various bioinformatics tasks [10] emboss.sourceforge.net DnaSP Analyze DNA sequence polymorphisms [11] www.ub.es/dnasp FASTA Database search [9] fasta.bioch.virginia.edu GenScan Gene prediction [3] genes.mit.edu/GENSCAN.html gff2aplot Plotting sequence comparisons [1] genome.imim.es/software

ms Coalescent simulations [6] home.uchicago.edu/~rhudson1 MUMmer Genomealignment [4] www.tigr.org/software PHYLIP Phylogeny reconstruction [5] evolution.genetics.washington.edu SGP-2 Gene prediction [8] www1.imim.es/software/sgp2 Slam Gene prediction [7] bio.math.berkeley.edu/slam

ICB ­c 2006 Birkhäuser Verlag Bioinformatics Databases

Name Purpose Website GenBank primary sequence repository www.ncbi.nlm.nih.gov EMBL primarysequencerepository www.ebi.ac.uk/embl DDBJ primarysequencerepository www.ddbj.nig.ac.jp SwissProt curated protein sequences www..org/sprot PDB macromolecular structures www.rcsb.org/pdb INTERPRO protein motifs www.ebi.ac.uk/

ICB ­c 2006 Birkhäuser Verlag References

J. F. Abril, R. Guigó, and T. Wiehe. gff2aplot: plotting sequence comparisons. Bioinformatics, 19:2477–2479, 2004. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. Basic local alignment search tool. Journal of Molecular Biology, 215:403–410, 1990. C. B. Burge and S. Karlin. Prediction of complete gene structures in human genomic DNA. Journal of Molecular Biology, 268:78–94, 1997. A. L. Delcher, S. Kasti, R. D. Fleischmann, J. Peterson, O. White, and S. L. Salzberg. Alignment of whole genomes. Nucleic Acids Research, 27:2369–2376, 1999. J. Felsenstein. PHYLIP (phylogeny interference package), 1993. R. R. Hudson. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics, 18:337–338, 2002. L. Pachter, M. Alexandersson, and S. Cawley. Applications of generalized pair Hidden Markov Models to alignment and gene finding problems. In Proceedings of the Fifth Annual Conference on Computational Molecular Biology (RECOMB 2001), pages 241–248. ACM Press, New York, 2001. G. Parra, P. Agarwal, J. F. Abril, T. Wiehe, J. Fickett, and R. Guigó. Comparative gene prediction in human and mouse. Genome Research, 13:108–117, 2003. W. R. Pearson and D. J. Lipman. Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences, USA, 85:2444–2448, 1988. P. Rice and A. Bleasby. EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics, 16:276–277, 2000. J. Rozas, J. C. Sánchez-DelBarrio, X. Messeguer, and R. Rozas. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19:2496–2497, 2003. J. D. Thompson, D. G. Higgins, and T. J. Gibson. W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalities and weight matrix choice. Nucleic Acids Research, 22:4673–4680, 1994.

ICB ­c 2006 Birkhäuser Verlag