Expressed sequence tags with cDNA termini: Previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii

Genetics

Volumn 179, Issue 1, 2008, Pages 83-93

  Liang, Chun ^a   Liu, Yuansheng ^a   Liu, Lin ^a   Davis, Adam C ^a   Shen, Yingjia ^a   Li, Qingshun Quinn ^a  

^a MIAMI UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; TRANSCRIPTOME;

ARTICLE; CHLAMYDOMONAS REINHARDTII; CONTROLLED STUDY; DNA LIBRARY; EXPRESSED SEQUENCE TAG; GENE SEQUENCE; GENE STRUCTURE; NONHUMAN; PRIORITY JOURNAL; RNA METABOLISM; ANIMAL; BIOLOGY; CHROMOSOME MAP; COMPARATIVE STUDY; GENE EXPRESSION PROFILING; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; UNTRANSLATED REGION;

CHLAMYDOMONAS REINHARDTII;

ANIMALS; BASE SEQUENCE; CHLAMYDOMONAS REINHARDTII; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; MOLECULAR SEQUENCE DATA; UNTRANSLATED REGIONS;

EID: 52049117699     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.085605     Document Type: Article

References (31)

1. ADZHUBEI, A. A., J. K. LAERDAHL and A. V. VLASOVA, 2006 pre-Assemble: a tool for automatic sequencer trace data processing. BMC Bioinformatics 7: 22.
2. ASAMIZU, E., Y. NAKAMURA, S. SATO, H. FUKUZAWA and S. TABATA, 1999 A large scale structural analysis of cDNAs in a unicellular green alga, Chlamydomonas reinhardtii. I. Generation of 3433 nonredundant expressed sequence tags. DNA Res. 6: 369-373.
3. ASAMIZU, E., K. MIURA, K. KUCHO, Y. INOUE, H. FUKUZAWA et al., 2000 Generation of expressed sequence tags from low-CO2 and high-CO2 adapted cells of Chlamydomonas reinhardtii. DNA Res. 7: 305-307.
4. ASAMIZU, E., Y. NAKAMURA, K. MIURA, H. FUKUZAWA, S. FUJIWARA et al., 2004 Establishment of publicly available cDNA material and information resource of Chlamydomonas reinhardtii (Chlorophyta), to facilitate gene function analysis. Phycologia 43: 722-726.
5. CHEN, Y. A., C. C. LIN, C. D. WANG, H. B. WU and P. I. HWANG, 2007 An optimized procedure greatly improves EST vector contamination removal. BMC Genomics 8: 416.
6. CHOU, H.-H., and M. H. HOLMES, 2001 DNA sequence quality trimming and vector removal. Bioinformatics 17: 1093-1104.
7. EWING, B., L. HILLIER, M. C. WENDL and P. GREEN, 1998 Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8: 175-185.
8. GOWDA, M., H. LI, J. ALESSI, F. CHEN, R. PRATT et al., 2006 Robust analysis of 5′-transcript ends (5′-RATE): a novel technique for transcriptome analysis and genome annotation. Nucleic Acids Res. 34: e126.
9. GRABER, J. H., C. R. CANTOR, S. C. MOHR and T. F. SMITH, 1999 In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species. Proc. Natl. Acad. Sci. USA 96: 14055-14060.
10. GROSSMAN, A. R., E. E. HARRIS, C. HAUSER, P. A. LEFEBVRE, D. MARTINEZ et al., 2003 Chlamydomonas reinhardtii at the crossroads of genomics. Eukaryot. Cell 2: 1137-1150.
11. HALL-POGAR, T., H. ZHANG, B. TIAN and C. S. LUTZ, 2005 Alternative polyadenylation of cyclooxygenase-2. Nucleic Acids Res. 33: 2565-2579.
12. JAIN, M., J. SHRAGER, E. H. HARRIS, R. HALBROOK, A. R. GROSSMAN et al., 2007 EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome. Nucleic Acids Res. 35: 2074-2083.
13. JIN, Y., and T. BIAN, 2004 Nontemplated nucleotide addition prior to polyadenylation: a comparison of Arabidopsis cDNA and genomic sequences. RNA 10: 1695-1697.
14. KENT, W. J., 2002 BLAT - the BLAST-like alignment tool. Genome Res. 12: 656-664.
15. LAMPERTI, E. D., J. M. KITTELBERGER, T. F. SMITH and L. VILLA-KOMAROFF, 1992 Corruption of genomic databases with anomalous sequence. Nucleic Acids Res. 20: 2741-2747.
16. LI, M., B. MA, D. KISMAN and J. TROMP, 2004 PatternHunter II: highly sensitive and fast homology search. J. Bioinform. Comput. Biol. 2: 417-440.
17. LIANG, C., F. SUN, H. WANG, J. QU, R. M. FREEMAN JR. et al., 2006 MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools. BMC Bioinformatics 7: 115.
18. LIANG, C., G. WANG, L. LIU, G. JI, L. FANG et al., 2007a WebTraceMiner: a web service for processing and mining EST sequence trace files. Nucleic Acids Res. 35: W137-142.
19. LIANG, C., G. WANG, L. LIU, G. JI, K. CARTER et al., 2007b ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs). BMC Genomics 8: 134.
20. LOKE, J. C., E. A. STAHLBERG, D. G. STRENSKI, B. J. HAAS, P. C. WOOD et al., 2005 Compilation of mRNA polyadenylation signals in arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol. 138: 1457-1468.
21. MERCHANT, S. S., S. E. PROCHNIK, O. VALLON, E. H. HARRIS, S. J. KARPOWICZ et al., 2007 The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318: 245-251.
22. NAGARAJ, S. H., R. B. GASSER and S. RANGANATHAN, 2006 A hitch-hiker's guide to expressed sequence tag (EST) analysis. Brief. Bioinformatics 8: 6-21.
23. SELUJA, G. A., A. FARMER, M. MCLEOD, C. HARGER and P. A. SCHAD, 1999 Establishing a method of vector contamination identification in database sequence. Bioinformatics 15: 106-110.
24. SHEN, Y., Y. LIU, L. LIU, C. LIANG and Q. Q. LI, 2008 Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii . Genetics 179: 167-176.
25. SHRAGER, J., C. HAUSER, C. W. CHANG, E. H. HARRIS, J. DAVIES et al., 2003 Chlamydomonas reinhardtii genome project. A guide to the generation and use of the cDNA information. Plant Physiol. 131: 401-408.
26. SMITH, T. F., and M. S. WATERMAN, 1981 Identification of common molecular subsequences. J. Mol. Biol. 147: 195-197.
27. STADEN, R., 1996 The Staden sequence analysis package. Mol. Biotechnol. 5: 233-241.
28. TATUSOVA, T. A., and T. L. MADDEN, 1999 BLAST 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174: 247-250.
29. WEI, C. L., P. NG, K. P. CHIU, C. H. WONG, C. C. ANG et al., 2004 5′ long serial analysis of gene expression (LongSAGE) and 3′ LongSAGE for transcriptome characterization and genome annotation. Proc. Natl. Acad. Sci. USA 101: 11701-11706.
30. WU, T. D., and C. K. WATANABE, 2005 GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21: 1859-1875.
31. ZHAO, J., L. HYMAN and C. MOORE, 1999 Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev. 63: 405-445.