PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs

被引：73

作者：

Fredslund, J

Schauser, L

Madsen, LH

Sandal, N

Stougaard, J

机构：

[1] Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus, Denmark

[2] Aarhus Univ, Dept Mol Biol, Lab Gene Express, DK-8000 Aarhus, Denmark

来源：

NUCLEIC ACIDS RESEARCH | 2005年 / 33卷

关键词：

D O I：

10.1093/nar/gki425

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Using a comparative approach, the web program PriFi (http://cgi-www.daimi.au.dk/cgi-chili/PriFi/main) designs pairs of primers useful for PCR amplification of genomic DNA in species where prior sequence information is not available. The program works with an alignment of DNA sequences from phylogenetically related species and outputs a list of possibly degenerate primer pairs fulfilling a number of criteria, such that the primers have a maximal probability of amplifying orthologous sequences in other phylogenetically related species. Operating on a genome-wide scale, PriFi automates the first steps of a procedure for developing general markers serving as common anchor loci across species. To accommodate users with special preferences, configuration settings and criteria can be customized.

引用

收藏

页码：W516 / W520

页数：5

相关论文

共 11 条

[1]

BURPO FJ, 2001, BIOCHEMISTRY-US, P218

[2] Estimating genome conservation between crop and model legume species [J].

Choi, HK ;

Mun, JH ;

Kim, DJ ;

Zhu, HY ;

Baek, JM ;

Mudge, J ;

Roe, B ;

Ellis, N ;

Doyle, J ;

Kiss, GB ;

Young, ND ;

Cook, DR .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (43) :15289-15294

[3] Primer design for large scale sequencing [J].

Haas, S ;

Vingron, M ;

Poustka, A ;

Wiemann, S .

NUCLEIC ACIDS RESEARCH, 1998, 26 (12) :3006-3012

[4] Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes [J].

Lyons, LA ;

Laughlin, TF ;

Copeland, NG ;

Jenkins, NA ;

Womack, JE ;

OBrien, SJ .

NATURE GENETICS, 1997, 15 (01) :47-56

[5] AcePrimer: automation of PCR primer design based on gene structure [J].

McKay, SJ ;

Jones, SJM .

BIOINFORMATICS, 2002, 18 (11) :1538-1539

[6] TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets [J].

Pertea, G ;

Huang, XQ ;

Liang, F ;

Antonescu, V ;

Sultana, R ;

Karamycheva, S ;

Lee, Y ;

White, J ;

Cheung, F ;

Parvizi, B ;

Tsai, J ;

Quackenbush, J .

BIOINFORMATICS, 2003, 19 (05) :651-652

[7] The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species [J].

Quackenbush, J ;

Cho, J ;

Lee, D ;

Liang, F ;

Holt, I ;

Karamycheva, S ;

Parvizi, B ;

Pertea, G ;

Sultana, R ;

White, J .

NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :159-164

[8] Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences [J].

Rose, TM ;

Schultz, ER ;

Henikoff, JG ;

Pietrokovski, S ;

McCallum, CM ;

Henikoff, S .

NUCLEIC ACIDS RESEARCH, 1998, 26 (07) :1628-1635

[9]

Rozen S, 2000, Methods Mol Biol, V132, P365

[10] Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes [J].

Sugimoto, N ;

Nakano, S ;

Yoneyama, M ;

Honda, K .

NUCLEIC ACIDS RESEARCH, 1996, 24 (22) :4501-4505