Sequence analysis made easy. Mallard is a program for screening 16S rRNA clone libraries, and similar multiple sequence alignments for chimeras and other anomalies.
The nature of DNA sequencing is such that artifacts are inevitably introduced and, for 16S rDNA, common errors are chimera formation, poor sequencing, and poor sequence assembly. The public repositories are compromised with these unreliable sequences. In addition, any new sequence generated is potentially anomalous.
Researchers need to be as confident as possible that the sequences they are handling are reliable. Undetected, anomalies can lead to misleading phylogenetic reconstruction, give a false impression of species diversity, and confuse attempts at species classification and identification.
The program is based on the Pintail algorithm which works by comparing evolutionary distances between a query and subject sequence over the length of the 16S rRNA gene (small subunit rRNA), by employing a sampling window of specified size, progressing a fixed number of bases at a time along the length of the gene.
A quick guide to using Mallard
1. From the File menu, select Open Sequence File and load a suitable input file.
2. Select Run to generate a DE plot of the supplied data.
3. Select Identify Outliers to identify outlier DE values and generate a list of likely anomalous sequences.
All other users: From the command line use the command: java -jar Mallard.jar
The license of this software is Free, you can free download and free use this calculator software.