ArticleBMC research notes2009
Perl module and PISE wrappers for the integrated analysis of sequence data and SNP features.
Article in BMC research notes, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Candidate gene analysis for determinacy in pigeonpea (Cajanus spp.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers.Frontiers in plant science · 2014Article
- Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.).Functional & integrative genomics · 2011Article
- Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2011Article
- The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.).BMC plant biology · 2010Article
- A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.).BMC genomics · 2009Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThere is a need for software scripts and modules for format parsing, data manipulation, statistical analysis and annotation especially for tasks related to marker identification from sequence data and sequence diversity analysis.
resultsHere we present several new Perl scripts and a module for sequence data diversity analysis. To enable the use of these software with other public domain tools, we also make available PISE (Pasteur Institute Software Environment) wrappers for these Perl scripts and module. This enables the user to generate pipelines for automated analysis, since PISE is a web interface generator for bioinformatics programmes.
conclusionA new set of modules and scripts for diversity statistic calculation, format parsing and data manipulation are available with PISE wrappers that enable pipelining of these scripts with commonly used contig assembly and sequence feature prediction software, to answer specific sequence diversity related questions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.