HaploSNPer: A web-based allele and SNP detection tool

BMC Genetics

Volumn 9, Issue , 2008, Pages

  Tang, Jifeng ^a   Leunissen, Jack A M ^a   Voorrips, Roeland E ^a   van der Linden, C Gerard ^a   Vosman, Ben ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CLUSTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; DIPLOIDY; EXPRESSED SEQUENCE TAG; GENETIC ALGORITHM; HAPLOTYPE; HUMAN; INTERNET; MATHEMATICAL COMPUTING; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYPLOIDY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; ALGORITHM; ANIMAL; GENETIC DATABASE; GENETICS; PLOIDY;

ALGORITHMS; ALLELES; ANIMALS; CLUSTER ANALYSIS; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; HAPLOTYPES; HUMANS; INTERNET; PLOIDIES; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 41849098550     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-9-23     Document Type: Article

References (23)

1. Syvanen AC Accessing genetic variation: Genotyping single nucleotide polymorphisms Nature Reviews Genetics 2001, 2:930-942. 10.1038/35103535 11733746
2. The International HapMap Consortium A haplotype map of the human genome Nature 2005, 437:1299-1320. 1880871 16255080 10.1038/nature04226
3. Halperin E Eskin E Haplotype reconstruction from genotype data using imperfect Phylogeny Bioinformatics 2004, 20:1842-1849. 10.1093/ bioinformatics/bth149 14988101
4. Rafalski A Applications of single nucleotide polymorphisms in crop genetics Current Opinion in Plant Biology 2002, 5:94-100. 10.1016/ S1369-5266(02)00240-6 11856602
5. Tang JT Vosman B Voorrips RE van der Linden GC Leunissen JAM QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/ deletions in EST data from diploid and polyploid species BMC bioinformatics 2006, 7:438-453. 1618865 17029635 10.1186/1471-2105-7-438
6. Russell J Booth A Fuller J Harrower B Hedley P Machray G Powell W A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome Genome 2004, 47:389-398. 15060592
7. Schneider K Weisshaar B Borchardt DC Salamini F SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes Molecular Breeding 2001, 8:63-74. 10.1023/A:1011902916194
8. Picoult-Newberg L Ideker TE Pohl MG Taylor S Donaldson MA Nickerson DA Boyce JM Mining SNP from EST databases Genome Research 1999, 9:167-174. 310719 10022981
9. Buetow KH Edmonson MN Cassidy AB Reliable identification of large numbers of candidate SNP from public EST data Nature Genetics 1999, 21:323-325. 10.1038/6851 10080189
10. Barker G Batley J O' Sullivan H Edwards KJ Edwards D Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP Bioinformatics 2003, 19:421-422. 10.1093/bioinformatics/btf881 12584131
11. Dantec LL Chagné D Pot D Cantin O Garnier-Géré P Bedon F Frigerio JM Chaumeil P Léger P Garcia V Automated SNP detection in expressed sequence tags: Statistical considerations and application to maritime pine sequences Plant Molecular Biology 2004, 54:461-470. 10.1023/B:PLAN.0000036376.11710.6f 15284499
12. Weckx S Del Favero J Rademakers R Claes L Cruts M De Jonghe P Van Broeckhoven C De Rijk P novoSNP, a novel computational tool for sequence variation discovery Genome Research 2005, 15:436-442. 551570 15741513 10.1101/gr.2754005
13. Savage D Batley J Erwin T Logan E Love CG Lim GA Mongin E Barker G Spangenberg G Edwards D SNPServer: A real-time SNP discovery tool Nucleic Acids Research 2005, 33:W493-495. 1160223 15980519 10.1093/nar/ gki462
14. Marth GT Korf I Yandell MD Yeh RT Gu Z Zakeri H Stitziel NO Hillier LD Kwok P Gish WR A general approach to single-nucleotide polymorphism discovery Nature Genetics 1999, 23:452-456. 10.1038/70570 10581034
15. Altschul SF Madden T Schaeffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Research 1997, 25:3389-3402. 146917 9254694 10.1093/nar/25.17.3389
16. Huang X Madan A CAP3: A DNA sequence assembly program Genome Research 1999, 9:868-877. 310812 10508846 10.1101/gr.9.9.868
17. Phrap http://www.phrap.org/
18. Ewing B Green P Base-calling of automated sequencer traces using phred. II. Error probabilities Genome Res 1998, 8:186-194. 9521922
19. Smit AFA Hubley R Green P http://repeatmasker.org/
20. Malde K Coward E Jonassen I A graph base algorithm for generating EST consensus sequences Bioinformatics 2005, 21:1371-1375. 10.1093/ bioinformatics/bti184 15572463
21. Pruitt KD Tatusova T Maglott DR NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Research 2007, 35:D61-D65. 1716718 17130148 10.1093/nar/gkl842
22. Van Herpen T Goryunova S van der Schoot J Mitreva M Salentijn E Vorst O Schenk M van Veelen P Koning F van Soest L Alpha-gliadin genes from the A, B, and D genomes of wheat contain different sets of celiac disease epitopes BMC Genomics 2006, 7:1-13. 1368968 16403227 10.1186/ 1471-2164-7-1
23. HaploSNPer http://www.bioinformatics.nl/tools/haplosnper/manuals/ HaploSNPer_manual.html