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Items: 11

1.
2.

Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK.

Nature. 2005 Apr 7;434(7034):724-31.

PMID:
15815621
3.

A genome-wide survey of human pseudogenes.

Torrents D, Suyama M, Zdobnov E, Bork P.

Genome Res. 2003 Dec;13(12):2559-67.

4.

RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences.

Wernersson R, Pedersen AG.

Nucleic Acids Res. 2003 Jul 1;31(13):3537-9.

5.

The Bioperl toolkit: Perl modules for the life sciences.

Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E.

Genome Res. 2002 Oct;12(10):1611-8.

6.
7.

PAML: a program package for phylogenetic analysis by maximum likelihood.

Yang Z.

Comput Appl Biosci. 1997 Oct;13(5):555-6. No abstract available.

PMID:
9367129
8.

Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison.

Birney E, Durbin R.

Proc Int Conf Intell Syst Mol Biol. 1997;5:56-64.

PMID:
9322016
10.

A codon-based model of nucleotide substitution for protein-coding DNA sequences.

Goldman N, Yang Z.

Mol Biol Evol. 1994 Sep;11(5):725-36.

PMID:
7968486

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