The Pig Genome Database (PiGenome): An integrated database for pig genome research

Mammalian Genome

Volumn 20, Issue 1, 2009, Pages 60-66

  Lim, Dajeong ^a,b   Cho, Yong Min ^b   Lee, Kyung Tai ^b   Kang, Yeonkyung ^a   Sung, Samsun ^a   Nam, Jungrye ^a   Park, Eung Woo ^b   Oh, Sung Jong ^b   Im, Seok Ki ^b   Kim, Heebal ^a  

^a Seoul National University   (South Korea)

^b National Institute of Animal Science   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ALTERNATIVE RNA SPLICING; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CONTIG MAPPING; DNA LIBRARY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE MAPPING; GENE SEQUENCE; GENETIC DATABASE; GENETIC MARKER; NONHUMAN; NUCLEOTIDE SEQUENCE; QUANTITATIVE TRAIT LOCUS; SEQUENCE TAGGED SITE; SINGLE NUCLEOTIDE POLYMORPHISM; SWINE; UNINDEXED SEQUENCE;

ALGORITHMS; ALTERNATIVE SPLICING; ANIMALS; BIOMEDICAL RESEARCH; CHROMOSOME MAPPING; DATABASES, GENETIC; GENE LIBRARY; GENOME; ORGAN SPECIFICITY; SWINE;

ANIMALIA; BACTERIA (MICROORGANISMS); SUIDAE;

EID: 58649100240     PISSN: 09388990     EISSN: 14321777     Source Type: Journal    
DOI: 10.1007/s00335-008-9156-3     Document Type: Article

References (30)

1. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389 3402
2. AL Archibald CS Haley JF Brown S Couperwhite HA McQueen 1995 The PiGMaP consortium linkage map of the pig (Sus scrofa) Mamm Genome 6 157 175
3. O Couronne A Poliakov N Bray T Ishkhanov D Ryaboy 2003 Strategies and tools for whole-genome alignments Genome Res 13 73 80
4. DJ de Koning LL Janss AP Rattink PA van Oers BJ de Vries 1999 Detection of quantitative trait loci for backfat thickness and intramuscular fat content in pigs (Sus scrofa) Genetics 152 1679 1690
5. B Ewing P Green 1998 Base-calling of automated sequencer traces using phred II. Error probabilities Genome Res 8 186 194
6. M Fang X Hu T Jiang M Braunschweig L Hu 2005 The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers Anim Genet 36 7 13
7. L Florea G Hartzell Z Zhang GM Rubin W Miller 1998 A computer program for aligning a cDNA sequence with a genomic DNA sequence Genome Res 8 967 974
8. D Gordon C Abajian P Green 1998 Consed: a graphical tool for sequence finishing Genome Res 8 195 202
9. J Gorodkin S Cirera J Hedegaard MJ Gilchrist F Panitz 2007 Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1, 021, 891 expressed sequence tags Genome Biol 8 R45
10. E Grindflek J Szyda Z Liu S Lien 2001 Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross Mamm Genome 12 299 304
11. J Hu C Mungall A Law R Papworth JP Nelson 2001 The ARKdb: genome databases for farmed and other animals Nucleic Acids Res 29 106 110
12. ZL Hu S Dracheva W Jang D Maglott J Bastiaansen 2005 A QTL resource and comparison tool for pigs: PigQTLDB Mamm Genome 16 792 800
13. X Huang A Madan 1999 CAP3: A DNA sequence assembly program Genome Res 9 868 877
14. JT Jeon EW Park HJ Jeon TH Kim KT Lee 2003 A large-insert porcine library with sevenfold genome coverage: a tool for positional cloning of candidate genes for major quantitative traits Mol Cells 16 113 116
15. H Kim D Lim BK Han S Sung M Jeon 2006 ChickGCE: a novel germ cell EST database for studying the early developmental stage in chickens Genomics 88 252 257
16. TH Kim NS Kim D Lim KT Lee JH Oh 2006 Generation and analysis of large-scale expressed sequence tags (ESTs) from a full-length enriched cDNA library of porcine backfat tissue BMC Genomics 7 36
17. C Ovilo M Perez-Enciso C Barragan A Clop C Rodriquez 2000 A QTL for intramuscular fat and backfat thickness is located on porcine chromosome 6 Mamm Genome 11 344 346
18. C Ovilo A Clop JL Noguera MA Oliver C Barragan 2002 Quantitative trait locus mapping for meat quality traits in an Iberian × Landrace F2 pig population J Anim Sci 80 2801 2808
19. GA Rohrer LJ Alexander Z Hu TP Smith JW Keele 1996 A comprehensive map of the porcine genome Genome Res 6 371 391
20. MF Rothschild 2003 From a sow's ear to a silk purse: real progress in porcine genomics Cytogenet Genome Res 102 95 99
21. J Ruan Y Guo H Li Y Hu F Song 2007 PigGIS: Pig Genomic Informatics System Nucleic Acids Res 35 D654 D657
22. Stapleton M, Carlson J, Brokstein P, Yu C, Champe M et al (2002) A Drosophila full-length cDNA resource. Genome Biol 3:RESEARCH0080
23. Y Suzuki K Yoshitomo-Nakagawa K Maruyama A Suyama S Sugano 1997 Construction and characterization of a full length-enriched and a 5-end-enriched cDNA library Gene 200 149 156
24. J Szyda Z Liu E Grindflek S Lien 2002 Application of a mixed inheritance model to the detection of quantitative trait loci in swine J Appl Genet 43 69 83
25. H Uenishi T Eguchi K Suzuki T Sawazaki D Toki 2004 PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries Nucleic Acids Res 32 D484 D488
26. JC Venter MD Adams GG Sutton AR Kerlavage HO Smith 1998 Shotgun sequencing of the human genome Science 280 1540 1542
27. P Vodicka K Smetana Jr B Dvorankova T Emerick YZ Xu 2005 The miniature pig as an animal model in biomedical research Ann N Y Acad Sci 1049 161 171
28. DP Wall HB Fraser AE Hirsh 2003 Detecting putative orthologs Bioinformatics 19 1710 1711
29. JE Womack 2005 Advances in livestock genomics: opening the barn door Genome Res 15 1699 1705
30. D Zhuo WD Zhao FA Wright HY Yang JP Wang 2001 Assembly, annotation, and integration of UNIGENE clusters into the human genome draft Genome Res 11 904 918