ESTviewer(click here to ESTviewer Web interface)

A Web interface for visualizing mouse, rat, cattle, pig, and chicken conserved ESTs in human genes and human alternatively spliced variants

Contact: Dr.Trees-Juen Chuang 

Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan

• PSEP combines CRASA-based alignment with comparative analysis between human and mouse to identify human gene structures and AS transcripts. PSEP differs from other comparative approaches in that it takes account of conserved sequences between the human genome and mouse ESTs, in addition to genome comparison between the two species. PSEP can also detect AS transcripts. The abilities to detect AS and perform comparative analysis make PSEP suitable for studying AS in the context of evolution. (Publication: Trees-Juen Chuang*, Feng-Chi Chen, and Meng-Yuan Chou, “A Comparative Method for Identification of Gene Structures and Alternatively Spliced Variants,” Bioinformatics, Vol. 20, No. 17, pp.3064-3079, 2004.)   
• The aligner used here is CRASA (Chuang et al., 2003). Unlike other EST-to-genome or genome-to-genome alignment tools such as BLASTZ (Schwartz et al., 2003), BLAT (Kent, 2002), SSAHA (Ning et al., 2001), MegaBlast (Zhang et al., 2000), or sim-x (Chao et al., 1995; 1997), CRASA requires that the target databases (e.g., EST or genome databases) be reconstructed using pattern-based processing and hashing (or indexing) with binary codes in a multi-level pyramidal structure. Then the reorganized target databases are maintained in pyramidal databases. Because of the multi-leveled pyramidal structure and the corresponding pattern-associated binary code system, the database is highly efficient and can be systematically managed. The low computational time complexity and the pyramid structure enable CRASA to perform parallel processing of query sequences without size limitation (Chuang et al., 2003).  (Publication:  Trees-Juen Chuang, Wen-Chang Lin, Hurng-Chun Lee, Chi-Wei Wang, Keh-Lin Hsiao, Zi-Hao Wang, Danny Shieh, Simon C. Lin, and Lan-Yang Ch’ang, "A Complexity Reduction Algorithm for Analysis and Annotation of Large Genomic Sequences," Genome Research, Vol. 13, No. 2, pp. 313-322, 2003.)

Data Download:

PSEP annotation==>   

Cross-species EST-to-human genome alignments==>

People:

PSEP programs ==> Trees-Juen Chuang, Feng-Chi Chen and Meng-Yuan Chou

ESTviewer Web interface ==> Trees-Juen Chuang and Feng-Chi Chen

Homepage maintained by Ms. Min_Chin Hsu

Last update: October 12, 2005