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Whether working on a model or non-model species for biomedical, economical or evolutionary research, next-generation sequencing has enabled biologists to rapidly generate a reference sequence for downstream applications and hypotheses generation. With the exception of a limited number of species, functional annotation is conducted by in-silico expe... moreriments based on sequence similarity. Some groups are also enriching their data with expression studies. JAMp is a platform that allows biologists to reclaim the analysis of transcript reconstruction experiments by providing an automated process for generating functional annotations and a user-friendly overview of these in-silico experiments. The entire software is built so that novice command-line users can take a transcriptome assembly and generate websites like those found in our demo.
Author: Alexie Papanicolaou and Temi Varghese (ExtJS viewer)
CSIRO Ecosystem Sciences
CSIRO Open Source Software Licence (Based on MIT/BSD Open Source Licence)
Broad Institute (United States), CSIRO (Australia), University of Western Sydney (Australia)
Papanicolaou, Alexie; Varghese, Temi (2014): Just_Annotate_My_proteins (JAMp). v1. CSIRO. Software Collection.
All Rights (including copyright) CSIRO Australia 2014.
The metadata and files (if any) are available to the public.
Apache web server; PHP; perl
Cont to TCP01 Dissecting Adaptive
This project seeks to deploy an analytical framework to conduct population transcriptomics analyses for the purpose of identifying genomic signatures relating the adaptive (or maladaptive) potential of a population in relation to a particular environment. We will make use of existing yet diverse capability across the enterprise in order to create a... more more efficient method of assessing adaptive potential based on transcriptomics and identify regions of relevance in species from natural ecosystems. less
genome annotation software development
The JAMg software was created to address the issue of creating gene models (feature annotation) and was built by Alexie Papanicolaou at the Commonwealth Scientific and Industrial Research Organisation (CSIRO) with some brilliant support from Brian Haas at the Broad Institute. The software and manual are written so that to guide the annotation proce... moress so that users can follow the process closely. Even though with JAMg you will not need another genome annotation pipeline, JAMg does not aim to replace other genome annotation pipelines (e.g. each sequencing center has its own): it does aim to support nascent genome annotators and (ultimately) educate its users about genome annotation in general. As part of our Just_Annotate series, JAMg links with JAMp and WebApollo to provide a first solution for users wishing to go from genome assembly to deriving biological hypotheses. less
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