About this tool

AS-EAST annotates and analyzes users' uploaded transcript data using the data stored in AS-ALPS.

Users can determine whether novel transcripts encode AS isoforms, and annotate functional domains and the interacting residues with other molecules in the AS isoforms.

Publications

If you use AS-EAST in your work, we request you to cite the following paper and the URL (http://as-alps.nagahama-i-bio.ac.jp/ASEAST/).

Masafumi Shionyu, Ken-ichi Takahashi, Mitiko Go, 2012. AS-EAST: a functional annotation tool for putative proteins encoded by alternatively spliced transcripts. Bioinformatics 28:2076-2077 [Abstruct]

Detection of AS regions

DataSet: ( Example of input sequence: Homo sapiens cDNA FLJ90159 fis, clone HEMBB1002465 )
Enter a nucleic acid sequence of query transcript (single-FASTA format)
or upload a FASTA file
Choose the prediction method for Coding Sequence (CDS):
Longest-ORF ( incomplete 5' terminus incomplete 3' terminus )

FrameDP: sensitive peptide prediction method on noisy matured sequences ( edit the noisy sequence to correct the frameshift )

Starting from the -th nt of the query transcript
Options:
No domain assignment with InterProScan

View the cache data of the input sequence (The cache data are stored for one week on the server.)

Generate an exon-skipped transcript sequence from a RefSeq transcript sequence

DataSet: for (e.g. PKM, IL4, LYPLA1) (e.g. 5315, 3565, 10434) (e.g. NM_010207, ENSMUST00000101095) (e.g. Fgfr2, Ctps2) (e.g. 14183, 55936) (e.g. NM_001170373, FBtr0075999) (e.g. ARY, Nrx-IV) (e.g. 3355076, 39387) (e.g. NM_065028, F52D10.3a.1) (e.g. hsp-60, ftt-2) (e.g. 175316, 181348) (e.g. NM_100718, AT2G42500.2) (e.g. CRT3, PP2A-4) (e.g. 837365, 818850) (e.g. XM_015755141, OS09T0124100-00) (e.g. LOC4346937, LOC9272621) (e.g. 4346937, 9272621)