LDA - a java-based linkage disequilibrium analyzer

نویسندگان

  • Keyue Ding
  • Kaixin Zhou
  • Fuchu He
  • Yan Shen
چکیده

UNLABELLED We describe an integrated java-based program that provides elaborate graphic and plain-text output of pairwise linkage disequilibrium (LD) analysis of single nucleotide polymorphisms genotypic data. It is most suitable for molecular geneticists, who are focusing on LD measures estimation, statistical significance test and extent prediction. AVAILABILITY The software is available at: http://www.chgb.org.cn/lda/lda.htm. SUPPLEMENTARY INFORMATION Detailed tutorials, LDA help system and examples are distributed within LDA software. For Macintosh OS X user, the Jre version 1.4 can be downloaded from http://connect.apple.com.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation

MOTIVATION Efficient models for genetic linkage disequilibrium (LD) are needed to enable appropriate statistical analysis of the dense, genome-wide single nucleotide polymorphism assays currently available. RESULTS Estimation of graphical models for LD within a restricted class of decomposable models is shown to be possible using computer time and storage that scale linearly with the number o...

متن کامل

Building chromosome-wide LD maps

SUMMARY BMapBuilder builds maps of pairwise linkage disequilibrium (LD) in either two or three dimensions. The optimized resolution allows for graphical display of LD for single nucleotide polymorphisms (SNPs) in a whole chromosome. AVAILABILITY The program is coded in Java, which runs on all relevant operating systems, including Windows, Mac and Unix/Linux, and is available from http://bios....

متن کامل

The Pattern of Linkage Disequilibrium in Livestock Genome

Linkage disequilibrium (LD) is bases of genomic selection, genomic marker imputation, marker assisted selection (MAS), quantitative trait loci (QTL) mapping, parentage testing and whole genome association studies. The Particular alleles at closed loci have a tendency to be co-inherited. In linked loci this pattern leads to association between alleles in population which is known as LD. Two metr...

متن کامل

Association mapping for resistance to powdery mildew in oriental tobacco (Nicotiana tabaccum L.) germplasm

Powdery mildew caused by Erysiphe cichoracearum is an important fungal disease which threatens tobacco (Nicotiana tabacum L.) production. The objective of this study was to determine DNA markers linked to genomic regions associated with resistance to powdery mildew in tobacco through the association mapping approach. Seventy tobacco geno-types were fingerprinted using 26 simple se-quence repeat...

متن کامل

Case-control genome-wide association study of rheumatoid arthritis from Genetic Analysis Workshop 16 using penalized orthogonal-components regression-linear discriminant analysis

Currently, genome-wide association studies (GWAS) are conducted by collecting a massive number of SNPs (i.e., large p) for a relatively small number of individuals (i.e., small n) and associations are made between clinical phenotypes and genetic variation one single-nucleotide polymorphism (SNP) at a time. Univariate association approaches like this ignore the linkage disequilibrium between SNP...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:
  • Bioinformatics

دوره 19 16  شماره 

صفحات  -

تاریخ انتشار 2003