MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools

Abstract

BackgroundProcessing raw DNA sequence data is an especially challenging task for relatively small laboratories and core facilities that produce as many as 5000 or more DNA sequences per week from multiple projects in widely differing species. To meet this challenge, we have developed the flexible, scalable, and automated sequence processing package described here.ResultsMAGIC-SPP is a DNA sequence processing package consisting of an Oracle 9i relational database, a Perl pipeline, and user interfaces implemented either as JavaServer Pages (JSP) or as a Java graphical user interface (GUI). The database not only serves as a data repository, but also controls processing of trace files. MAGIC-SPP includes an administrative interface, a laboratory information management system, and interfaces for exploring sequences, monitoring quality control, and troubleshooting problems related to sequencing activities. In the sequence trimming algorithm it employs new features designed to improve performance with respect to concerns such as concatenated linkers, identification of the expected start position of a vector insert, and extending the useful length of trimmed sequences by bridging short regions of low quality when the following high quality segment is sufficiently long to justify doing so.ConclusionMAGIC-SPP has been designed to minimize human error, while simultaneously being robust, versatile, flexible and automated. It offers a unique combination of features that permit administration by a biologist with little or no informatics background. It is well suited to both individual research programs and core facilities.

WebTraceMiner: a web service for processing and mining EST sequence trace files

“…Although general users are only required to furnish sequence information for the canonical model of directional cDNA library construction, advanced users have many different options for configuration to customize their trace processing events. For example, different criteria have been adopted in other software for the detection of polyA/T tails in ESTs (8,10,13,18,19). To investigate the impact of these different criteria, a user might want to compare polyA/T detection using two different criteria, e.g., a minimum length of 12 bases with 2 base maximum internal errors versus a minimum length of 8 continuous bases without any error base.…”

“…For example, preAssemble, which utilizes Pregap4 of the open-source STADEN package (5), proves to be problematic sometimes in detecting polyA/T tails shorter than 10 bases (14). For adapter/linker detection, MAGIC-SPP (13) does a better job than other existing packages, including TIGR Lucy (6), but has problems with inserts having more than two concatenated adapters. Adopting a different approach, WebTraceMiner first detects in an unbiased fashion all vector fragments, restriction sites, adapter/linker sequences and polyA or polyT runs in each sequence read as putative features.…”

“…Many software packages are available for processing raw EST traces prior to GenBank dbEST submission (5–13). Before such submission, EST sequences are typically screened and trimmed of vector, adapter/linker sequences and insert-flanking restriction endonuclease recognition sites, as well as polyA or polyT tails; however, available sequence processing packages are limited in their ability to detect and trim such sequences correctly (13,14). Loss of the information in these trimmed sequences can present an obstacle for data validation of error-prone ESTs, and can impede data mining for certain functional motifs, such as polyadenylation signals, whose detection requires accurate annotation of positional information for polyA tails added posttranscriptionally.…”

Characterization of Apomictic BC7 and BC8 Pearl Millet: Meiotic Chromosome Behavior and Construction of an ASGR‐carrier Chromosome‐specific Library

“…of Georgia, Athens) for sequencing using the T7 primer. Each sequencing reaction was given a unique name and processed for quality using the MAGIC processing pipeline and database (Liang et al, 2006). Sequences were screened for the multiple cloning site in the vector, for E. coli genomic DNA, and for human genomic DNA.…”

A Functional Genomics Investigation of Allelochemical Biosynthesis in Sorghum bicolor Root Hairs

“…5Ј DNA sequencing reactions were performed using ABI BigDye Terminator Cycle Sequence Ready Reaction kits (versions 2 and 3; Applied Biosystems, Foster City, CA) as described previously (26). Base calling on raw sequence trace data were performed using PHRED software (27), and vector, adapter, and low quality sequence ends were identified using an in-house processing script (28), resulting in 5,468 high quality sequences, or an 82.6% success rate. The average trimmed EST length, determined using a moving window with a PHRED quality score of 16, was 451 bp, of which on average 432 bp were called with a quality score equal to or greater than 20.…”