Introduction

The purpose of this service is to facilitate the utilization of the PsbA-TrnH Intergenic Spacer (psba-trnh igs) Regions in various DNA barcoding studies. Sequences were processed and assembled as described in our manuscipt. Basically, plant sequences associated with key words related to "psba-trnh igs" were retrieved from GenBank and were subjected to several steps of filtering. At last, sequences flanking the psba-trnh igs regions were removed and sequences that belong to the same species (indicated by having same taxonomy id, or taxid in short in the following text) were assembled. The consensus sequences of the sequence clusters were considered as the average or reference sequences (ref_bc) of the psba-trnh igs regions for individual species respectively. This web application consists of the following analytic modules to facilitate analysis based on these sequences:

1. View

This module shows all sequences associated with a taxonomy id (taxid) and also display the reference psba-trnh igs regions.

2. Retrieve

This module allows the user to retrieve various segments of the psba-trnh igs region (the psba gene segment, the psba-trnh igs core region, the trnh gene segment respectively).

3. Annotate

This module annotates the psba gene, the psba-trnh igs core region, the trnh gene for novel sequences. The user needs to provide the multiple alignments of sequences for the psba gene and the trnh gene. The module would then build Hidden Markov Models (HMM) with these fragments and use the HMM model to query the input sequences to define the boundaries of the various fragments.

4. Identify

This module will perform a blast search on a query sequence against our internal psba-trnh igs reference database. The top hit usually indicates the species to whom the input sequence belong to.


For questions and comments, please send email to cliu@implad.ac.cn or cliu6688@yahoo.com.

Center for Bioinformatics
Institute of Medicinal Plant Development
PeKing Union Medical College
Chinese Academy of Medical Sciences
Address: No. 151, Malianwa North Road, Haidian District, Beijing 100094, P.R.China
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