Analysis of 14 BAC sequences from the Aedes aegypti genome: A benchmark for genome annotation and assembly

Genome Biology

Volumn 8, Issue 5, 2007, Pages

  Lobo, Neil F ^a   Campbell, Kathy S ^b   Thaner, Daniel ^a   deBruyn, Becky ^a   Koo, Hean ^c   Gelbart, William M ^b   Loftus, Brendan J ^b   Severson, David W ^a   Collins, Frank H ^a  

^a UNIVERSITY OF NOTRE DAME   (United States)

^b HARVARD UNIVERSITY   (United States)

^c J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AEDES AEGYPTI; ANOPHELES GAMBIAE; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; DROSOPHILA MELANOGASTER; EXPRESSED SEQUENCE TAG; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENOME; HAPLOTYPE; INSECT GENETICS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SYNTENY; AEDES; ANIMAL; GENETICS; GENOMICS; METHODOLOGY; NUCLEIC ACID DATABASE;

AEDES AEGYPTI; ANOPHELES GAMBIAE; BACTERIA (MICROORGANISMS); DENGUE VIRUS GROUP; DROSOPHILA MELANOGASTER;

MESSENGER RNA;

AEDES; ANIMALS; BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; DATABASES, NUCLEIC ACID; GENOME; GENOMICS; POLYMORPHISM, GENETIC; RNA, MESSENGER;

EID: 34548813410     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-5-r88     Document Type: Article

References (20)

1. Broad Institute http://www.broad.mit.edu
2. The Institute for Genomic Research http://www.tigr.org
3. Batzoglou S Jaffe DB Stanley K Butler J Gnerre S Mauceli E Berger B Mesirov JP Lander ES ARACHNE: A whole-genome shotgun assembler. Genome Res 2002 12 177-189 155255 11779843 10.1101/gr.208902
4. VectorBase: An NIAID Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens http://vectorbase.org
5. Hillier LW Coulson A Murray JI Bao Z Sulston JE Waterston RH Genomics in C. elegans: So many genes, such a little worm. Genome Res 2005 15 1651-1660 10.1101/gr.3729105 16339362
6. Adams MD Celniker SE Holt RA Evans CA Gocayne JD Amanatides PG Scherer SE Li PW Hoskins RA Galle RF The genome sequence of Drosophila melanogaster. Science 2000 287 2185-2195 10.1126/science.287.5461.2185 10731132
7. Holt RA Subramanian GM Halpern A Sutton GG Charlab R Nusskern DR Wincker P Clark AG Ribeiro JM Wides R The genome sequence of the malaria mosquito Anopheles gambiae. Science 2002 298 79 10.1126/science.1076181 12364774
8. Sharakhova MV Hammond MP Lobo NF Krzywinski1 J Unger MF Hillenmeyer ME Bruggner RV Birney E Collins FH Update of the Anopheles gambiae PEST genome assembly. Genome Biol 2007 8 R5 1839121 17210077 10.1186/ gb-2007-8-1-r5
9. Severson DW Meece JK Lovin DD Saha G Morlais I Linkage map organization of expressed sequence tags and sequence tagged sites in the mosquito, Aedes aegypti. Insect Mol Biol 2002 11 371-378 10.1046/ j.1365-2583.2002.00347.x 12144703
10. Swindell SR Plasterer TN SEQMAN. Contig assembly. Methods Mol Biol 1997 70 75-89 9089604
11. Tu Z Genomic and evolutionary analysis of Feilai, a diverse family of highly reiterated SINEs in the yellow fever mosquito, Aedes aegypti. Mol Biol Evol 1999 16 760-772 10368954
12. Burge C Karlin S Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997 268 78-94 10.1006/jmbi.1997.0951 9149143
13. Salamov AA Solovyev VV Ab initio gene finding in Drosophila genomic DNA. Genome Res 2000 10 516-522 310882 10779491 10.1101/gr.10.4.516
14. Lewis SE Searle SM Harris N Gibson M Lyer V Richter J Wiel C Bayraktaroglu L Birney E Crosby MA Apollo: A sequence annotation editor. Genome Biol 2002 3 research0082.1 0082.14 10.1186/ gb-2002-3-12-research0082
15. Warren AM Crampton JM The Aedes aegypti genome: Complexity and organization. Genet Res 1991 58 225-232 1802804
16. RepeatMasker Open-3.0 http://www.repeatmasker.org
17. Jurka J Klonowski P Dagman V Pelton P CENSOR - a program for identification and elimination of repetitive elements from DNA sequences. Comput Chem 1996 20 119-122 10.1016/S0097-8485(96)80013-1 8867843
18. Severson DW DeBruyn B Lovin DD Brown SE Knudson DL Morlais I Comparative genome analysis of the yellow fever mosquito Aedes aegypti with Drosophila melanogaster and the malaria vector mosquito Anopheles gambiae. J Hered 2004 95 103-113 10.1093/jhered/esh023 15073225
19. Jimenez LV Kang BK deBruyn B Lovin DD Severson DW Characterization of an Aedes aegypti bacterial artificial chromosome (BAC) library and chromosomal assignment of BAC clones for physical mapping quantitative trait loci that influence Plasmodium susceptibility. Insect Mol Biol 2004 13 37-44 10.1046/j.0962-1075.2004.00456.x 14728665
20. National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov