Frequently Asked Questions about the ASFinder Server
About the author
The ASFinder (AS-Finder) server was implemented by Dr. Xiang Jia (Jack) Min in the Bioinformatics Laboratory, Proteomics/Genomics Research Group,Youngstown State University (YSU). The work was supported by the YSU Research Professorship award (2009 - 2010) and the STEM Dean's Reassigned Time.
Generating expressed sequence tags (ESTs) remains a primary method for gene discovery in most organisms. Identifying alternatively spliced transcript isoforms of a gene is an important step in gene functional annotation and for downstream experimental chracterization. The server is designed for identifying alternatively spliced transcripts from EST-derived sequences. Note: This server can be used for mapping ESTs to the genome (from which where the ESTs were derived), but it is not designed for predicting alternatively spliced genes from genomic sequences only.
How does it work?
If a genomic sequence file (with multiple sequences in fasta format) is provided by a user, EST-derived sequences (ESTs including cDNAs) will be mapped to the genomic sequences using SIM4 software. ESTs mapped to the same genomic locus and overlapped a certain length with a high similarity (two parameters chosen by a user) and also having exon/intron variations in the overlapping region are treated as "alternatively spliced" transcripts from a single gene. However, if no genomic sequences are provided, the ESTs will be used to perform a self-BLASTN, that is, NCBI-BLASTN will be performed to use the set of ESTs as both a "query" and a "database". ESTs having high similarities at both ends but having an unaligned internal fragment are treated as "alternatively spliced" transcripts.
If only ESTs are provided, the output files include (1) BLASTN output file, (2) AS clusters (alternatively splited transcripts clusters), (3) a multiple sequence alignment (MSA) file for AS isoforms generated by MUSCLE. If genomic sequences are provided, the output files include (1) SIM4 alignment file, (2) a file with a modified GTF (gene transfer format) format containing tab-delimited alignment information for all ESTs, (3) AS clusters, and (4) AS specific gtf file (AS.gtf) which contains EST alignment informatin of AS transcripts. The accuracies of the methods implemented in the server were evaluated using Aspergillus niger EST data and Arabidopsis mRNA sequences and the results were reported in the paper (Min 2013).
Security and confidentiality of user submitted data
The data submitted to our server will be automatically deleted after the output files are generated. We do not keep data submitted by a user.
How to obtain user's results
The results can be downloaded from the server web site. The results will be only kept on the site for 2 days after data processing, then it will be deleted.
How to cite us
Min, X.J. (2013) ASFinder: a tool for genome-wide identification of alternatively spliced transcripts from EST-derived sequences. International Journal of Bioinformatics Research and Applications. The webserver website http://bioinformatics.ysu.edu/tools/ASFinder.html can also be used as a reference.
The following papers have used ASFinder:
Stand-alone tool for download
The standalone version of the software is available free for academic use only. It is written in Perl and need to run in LINUX for the SIM4 software. Please download at following site for downloading.
Comments and suggestions
Please contact Dr. Min in the YSU Bioinformatics Lab.
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