Simple high-throughput annotation pipeline (SHAP)
نویسندگان
چکیده
SUMMARY SHAP (simple high-throughput annotation pipeline) is a lightweight and scalable sequence annotation pipeline capable of supporting research efforts that generate or utilize large volumes of DNA sequence data. The software provides Grid capable analysis, relational storage and Web-based full-text searching of annotation results. Implemented in Java, SHAP recognizes the limited resources of many smaller research groups. AVAILABILITY Source code is freely available under GPLv3 at https://sourceforge.net/projects/shap. CONTACT [email protected]; [email protected].
منابع مشابه
Bioinformatics for plant genome annotation
High throughput sequencing must be matched by high throughput annotation. Given the large number of annotation tools available, a multitude of interdependent analyses are required for an in-depth annotation of even a single BAC sequence. Special annotation pipeline software is required to make such annotation processes feasible in an automated fashion. In terms of functionality, such software s...
متن کاملA Web-based High-Throughput Tool for Next-Generation Sequence Annotation
The availability of a large number of genome sequences, resulting from inexpensive, high-throughput next-generation sequencing platforms, has created the need for an integrated, fully-automated, rapid, and high-throughput annotation capability that is also easy-to-use. Here, we present a web-based software application, Annotation of Genome Sequences (AGeS), which incorporates publicly-available...
متن کاملAn integrated pipeline for protein classification using specific PSSMs and existing protein annotations
Protein classification has been performed by many protein databases to infer annotations of unknown proteins and therefore enhance the performance of protein annotation. In this study, we implemented an integrated pipeline for protein classification using specific PSSMs and proteins with the same entity name. After clustering sequences on the basis of their evolutionary distances, a target grou...
متن کاملDDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data
High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecular biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analyti...
متن کاملMToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing
MOTIVATION The increasing availability of mitochondria-targeted and off-target sequencing data in whole-exome and whole-genome sequencing studies (WXS and WGS) has risen the demand of effective pipelines to accurately measure heteroplasmy and to easily recognize the most functionally important mitochondrial variants among a huge number of candidates. To this purpose, we developed MToolBox, a hi...
متن کاملذخیره 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 27 17 شماره
صفحات -
تاریخ انتشار 2011