PALS db: Putative Alternative Splicing database

Abstract

PALS db is a collection of Putative Alternative Splicing information from 19 936 human UniGene clusters and 16 615 mouse UniGene clusters. Alternative splicing (AS) sites were predicted by using the longest messenger RNA (mRNA) sequence in each UniGene cluster as the reference sequence. This sequence was aligned with related sequences in UniGene and dbEST to reveal the AS. This information was presented with six features: (i) literature aliases were used to improve the result of a gene name search; (ii) the quality of a prediction can be easily judged from the color-coded similarity and the scaled length of an alignment; (iii) we have clustered those EST sequences that support the same AS site together to enhance the users' confidence on a prediction; (iv) the users can also set up the alignment criteria interactively to recover false negatives; (v) tissue distribution can be displayed by placing the mouse cursor over an alignment; (vi) gene features will be analyzed at foreign sites by submitting the selected mRNA or its encoded protein as a query. Using these features, the users cannot only discover putative AS sites in silico, but also make new observations by combining AS information with tissue distributions or with gene features. PALS db is available at http://palsdb.ym.edu.tw/.

Figure 1

Major alignment types in predicting AS sites. (A) Alternative splicing may occur as exon skipping, alternative 5′ splicing donor sites and alternative 3′ acceptor sites (left panel from top to bottom). All three mechanisms may generate two alternative transcripts in which one of them (transcript 1) contains an extra fragment of sequence compared to transcript 2. By using mRNA as reference sequence, we could compare the difference between transcripts and discover putative AS sites (right panel). (B) In PALS db, the longest mRNA sequence in a UniGene cluster was used as the reference sequence to predict AS sites. The reference sequence (Seq1) was aligned with another transcript, which is in the form of either an EST sequence or an mRNA sequence (Seq2). The lengths of the matched regions on the left and right sides of an AS site were named ‘Len1’ and ‘Len2’, respectively. In type I, the reference sequence (Seq1) is like transcript 1 in (A). In type II, Seq2 (the sequence containing AS information) is like transcript 1 in (A). Pos1 and Pos2 mark locations of an AS site on the reference sequence. Pos3 and Pos4 mark locations of an AS site on the EST or mRNA sequences. In type III, combination of the three mechanisms described in (A) may cause unaligned sequences on both Seq1 and Seq2.

Figure 2

Graphic summary of the alternative splicing information for the gene EIF3S9. Each horizontal bar is an EST-reference sequence alignment. The quality of alignment is color-coded. Type one and type two AS sites (Fig. 1) are characterized by two dashed lines and by a vertical line in the middle, respectively. The number of EST sequences that support a given site is shown in front of each bar. The positions of a given site are listed at the end of each bar. Those AS sites that pass the threshold are marked by asterisks. The pale blue block and the blue scale bar are the coding region and the positions on the protein sequence, respectively. The ‘Details’, ‘Text’, ‘Search again!’ and ‘Help’ buttons on the top will connect to the detailed alternative splicing information in graphics, the text information, the query interface and the user’s guide, respectively. The ‘Similarities’ button will connect to the summary page of a human gene to a paralogous gene in mouse and vice versa. The rest buttons will submit either the nucleic acid or amino acid sequence of the reference sequence to foreign web sites for further analysis.