SeqHelp：一个利用普通计算资源分析分子序列的程序。
SeqHelp: a program to analyze molecular sequences utilizing common computational resources.
作者信息
Lee M K, Lynch E D, King M C
机构信息
Departments of Medicine and Genetics, University of Washington, Seattle, Washington 98195-7720, USA.
出版信息
Genome Res. 1998 Mar;8(3):306-12. doi: 10.1101/gr.8.3.306.
Abstract
Here we describe a tool to analyze molecular sequences utilizing the internet and existing computational resources for molecular biology. The computer program SeqHelp organizes information from database searches, gene structure prediction, and other information to generate multiply aligned, hypertext-linked reports to allow for fast analysis of molecular sequences. The efficient and economical strategy in this program can be employed to study molecular sequences for gene cloning, mutation analysis, and identical sequence search projects.
摘要
在此，我们描述一种利用互联网和现有的分子生物学计算资源来分析分子序列的工具。计算机程序SeqHelp整理来自数据库搜索、基因结构预测及其他信息，以生成多重比对、超文本链接的报告，从而实现对分子序列的快速分析。该程序中高效且经济的策略可用于基因克隆、突变分析及同源序列搜索项目的分子序列研究。
相似文献
1
SeqHelp: a program to analyze molecular sequences utilizing common computational resources.
Genome Res. 1998 Mar;8(3):306-12. doi: 10.1101/gr.8.3.306.
2
Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals.
BMC Bioinformatics. 2005 May 3;6:111. doi: 10.1186/1471-2105-6-111.
3
GATA: a graphic alignment tool for comparative sequence analysis.
BMC Bioinformatics. 2005 Jan 17;6:9. doi: 10.1186/1471-2105-6-9.
4
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8. doi: 10.1093/nar/gkm286. Epub 2007 May 7.
5
Computational analysis of transposable element sequences.
Methods Mol Biol. 2004;260:59-71. doi: 10.1385/1-59259-755-6:059.
6
Multiple alignment of DNA sequences with MAFFT.
Methods Mol Biol. 2009;537:39-64. doi: 10.1007/978-1-59745-251-9_3.
7
Mouse cytokine gene nucleotide sequence alignments, 2000. Part I.
Eur J Immunogenet. 2000 Aug;27(4):165-223. doi: 10.1046/j.1365-2370.2000.00217.x.
8
A tool for analyzing and annotating genomic sequences.
Genomics. 1997 Nov 15;46(1):37-45. doi: 10.1006/geno.1997.4984.
9
Sequence alignment and database searching.
Methods Biochem Anal. 2001;43:187-214. doi: 10.1002/0471223921.ch8.
10
transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences.
BMC Bioinformatics. 2005 Jun 22;6:156. doi: 10.1186/1471-2105-6-156.
引用本文的文献
1
Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population.
Hum Genomics. 2006 Jan;2(4):203-11. doi: 10.1186/1479-7364-2-4-203.
2
From flies' eyes to our ears: mutations in a human class III myosin cause progressive nonsyndromic hearing loss DFNB30.
Proc Natl Acad Sci U S A. 2002 May 28;99(11):7518-23. doi: 10.1073/pnas.102091699.
3
Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential.
Genome Res. 2001 Aug;11(8):1441-52. doi: 10.1101/gr.184001.
4
A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.
Genome Biol. 2001;2(4):RESEARCH0011. doi: 10.1186/gb-2001-2-4-research0011. Epub 2001 Mar 22.
5
MHC class II pseudogene and genomic signature of a 32-kb cosmid in the house finch (Carpodacus mexicanus).
Genome Res. 2000 May;10(5):613-23. doi: 10.1101/gr.10.5.613.
本文引用的文献
1
Base-calling of automated sequencer traces using phred. II. Error probabilities.
Genome Res. 1998 Mar;8(3):186-94.
2
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
Genome Res. 1998 Mar;8(3):175-85. doi: 10.1101/gr.8.3.175.
3
Nonsyndromic deafness DFNA1 associated with mutation of a human homolog of the Drosophila gene diaphanous.
Science. 1997 Nov 14;278(5341):1315-8.
4
Genotator: a workbench for sequence annotation.
Genome Res. 1997 Jul;7(7):754-62. doi: 10.1101/gr.7.7.754.
5
PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and annotation.
Genome Res. 1997 Jun;7(6):649-56. doi: 10.1101/gr.7.6.649.
6
Complete genomic sequence and analysis of 117 kb of human DNA containing the gene BRCA1.
Genome Res. 1996 Nov;6(11):1029-49. doi: 10.1101/gr.6.11.1029.
7
Entrez: molecular biology database and retrieval system.
Methods Enzymol. 1996;266:141-62. doi: 10.1016/s0076-6879(96)66012-1.
8
Recognizing exons in genomic sequence using GRAIL II.
Genet Eng (N Y). 1994;16:241-53.
9
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.
Gene. 1988 Dec 15;73(1):237-44. doi: 10.1016/0378-1119(88)90330-7.
10
Basic local alignment search tool.
J Mol Biol. 1990 Oct 5;215(3):403-10. doi: 10.1016/S0022-2836(05)80360-2.
Zotero 插件