PALMapper, the fusion of the short read mapper GenomeMapper [1] and the short read aligner QPALMA [2], is an easy-to-use and flexible tool to accurately and efficiently align both transcriptome reads (spliced and unspliced) from RNA-Seq experiments against a reference genome. PALMapper is able to take advantage of read-quality information by using the efficient training algorithm of QPALMA. It is additionally able to benefit from computational splice-site predictions which can be computed via ASP or mGene to improve the alignment accuracy.

PALMapper can be used on the command line or through a Web service, which is a customized version of the Galaxy framework [3].

A comprehensive tutorial about PALMapper appeared in December 2010 in Current Protocols in Bioinformatics (Unit 11.6) [4] and is available online here.

Working with PALMapper

PALMapper on the command-line

To use PALMapper on the command-line, go to https://public.bmi.inf.ethz.ch/software/ and download the last version of the following software, unpack and install them by following the given instructions:

PALMapper with Galaxy system

To use PALMapper with the Galaxy system, go to http://galaxy.raetschlab.org/


Data example

Data used in the tutorial consist of a random subset of 250,000 reads 36 nucleotides length from a real data example on Caenorhabditis elegans [5]. This example can be downloaded in its entirety from the NCBI Sequence Read Archive Web site (http://www.ncbi.nlm.nih.gov/sra) under accession number SRA003622 (experiment SRX001872).

The read data subset used as example in the tutorial as well as the genome sequence, the annotation file, the splice site predictions and QPALMA parameters are available as a Galaxy data library under the name "CP Bioinformatics - Example" and accessible via http://galaxy.raetschlab.org/library.

Splice site predictions

The user can take advantage of computational splice-site predictions to improve alignment accuracy. These predictions can be computed with ASP or mGene. The user can also directly download precomputed splice-site predictions for a growing list of organisms at http://ftp.raetschlab.org/resources/splice.


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[1] Schneeberger, K. et al., Simultaneous alignment of short reads against multiple genomes, Genome Biol. 10 (9):R98, 2009.
[2] De Bona, F. et al., Optimal Spliced Alignments of Short Sequence Reads, ECCB08/Bioinformatics, 24 (16):i174, 2008.
[3] Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A., and Taylor, J., Galaxy: A Web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. 89:19.10.1-19.10.21, 2010.
[4] Jean, G., Kahles, A., Sreedharan, V.T., De Bona, F., Raetsch, G., RNA-Seq Read Alignments with PALMapper, Curr. Protoc. Bioinform., 32:11.6.1-11.6.38, 2010.
[5] Hillier, L.W., Reinke, V., Green, P., Hirst, M., Marra, M.A., and Waterston, R.H., Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res. 19:657-666, 2009.