Effects of sample re-sequencing and trimming on the quality and size of assembled consensus sequences

Genetics and Molecular Research

Volumn 6, Issue 4, 2007, Pages 756-765

  Prosdocimi, F ^a   Lopes, D A O ^a   Peixoto, F C ^a   Mourao M M ^a   Pacifico L G G ^a   Ribeiro, R A ^a   Ortega, J M ^a  

^a FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

Author keywords

Assembling; CAP3; Codifying sequences; Consensus; PHRED; Sequencing reads; Trimming

Indexed keywords

ANALYTICAL ERROR; AUTOANALYSIS; COMPUTER PROGRAM; CONFERENCE PAPER; CONSENSUS SEQUENCE; DNA SEQUENCE; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS;

BASE PAIR MISMATCH; BASE SEQUENCE; CONSENSUS SEQUENCE; PLASMIDS; SEQUENCE ANALYSIS, DNA;

EID: 37349002424     PISSN: None     EISSN: 16765680     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (17)

1. Adams MD, Kelley JM, Gocayne JD, Dubnick M, et al. (1991). Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252: 1651-1656.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
3. Chen T and Skiena SS (2000). A case study in genome-level fragment assembly. Bioinformatics 16: 494-500.
4. Ewing B and Green P (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194.
5. Ewing B, Hillier L, Wendl MC and Green P (1998). Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185.
6. Franco GR, Rabelo EM, Azevedo V, Pena HB, et al. (1997). Evaluation of cDNA libraries from different developmental stages of Schistosoma mansoni for production of expressed sequence tags (ESTs). DNA Res. 4: 231-240.
7. Gordon D, Abajian C and Green P (1998). Consed: a graphical tool for sequence finishing. Genome Res. 8: 195-202.
8. Green P (1998). Documentation for PHRAP and cross-match. http://www.phrap.org/phrap.docs/phrap.html. Accessed November 3, 2007.
9. Huang X and Madan A (1999). CAP3: A DNA sequence assembly program. Genome Res. 9: 868-877.
10. MGC (Mammalian Gene Collection) Program Team (2002). Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. PNAS 99: 16899-16903.
11. Prosdocimi F and Ortega JM (2005). Accessing optimal primer distance from insert. In Silico Biol. 5: 469-477.
12. Prosdocimi F, Peixoto FC and Ortega JM (2003). DNA sequences base calling by PHRED: error pattern analysis. R. Tecnol. Inf. 3: 107-110.
13. Prosdocimi F, Peixoto FC and Ortega JM (2004). Evaluation of window cohabitation of DNA sequencing errors and lowest PHRED quality values. Genet. Mol. Res. 3: 483-492.
14. README for stand-alone BLAST. ftp://ftp.ncbi.nlm.nih.gov/blast/documents/ blastall.html. Accessed January 1, 2006.
15. Richterich P (1998). Estimation of errors in "raw" DNA sequences: a validation study. Genome Res. 8: 251-259.
16. Strausberg RL, Feingold EA, Klausner RD and Collins FS (1999). The mammalian gene collection. Science 286: 455-457.
17. Walther D, Bartha G and Morris M (2001). Basecalling with life trace. Genome Res. 11: 875-888.