Putative ALternative Splicing Database 
(PALS db)

[Introduction] [Rationale] [History]

[User's Guide] [AS Lists] [Text Info] [All Seq Info] [Hyperlinks] [Related db]

User's Guide

The UPDATED help material of Putative ALternative Splicing Database (PALS db) for Nucleic Acids Res. Database Issue 2002

Contents

1. Rationale
2. Audience of PALS db
3. Steps to use PALS db
   • Query interface
     • Select search field
     • Keyword and logic operation
     • Set the optional parameters
   • Search Results
     • AS lists
     • Text_Info
     • All Seq Info
     • Hyperlinks
   • Genes containing at least 20 ASSPs in PALS db Release 2
4. Release note
5. Statistics
   • Data sources
   • AS sites
6. Abbreviations
7. For updates, see User's guide
8. Disclaimer

Audience of PALS db

This database is designed for biologists, who are interested in

• Discovering biological phenomenon
• Solving a biological problem

PALS db is NOT designed to collect splicing site information for gene prediction programs.

Steps to use PALS db

1. Select search field [next step] [top]

• "Gene description + Gene name": the gene symbol and gene name approved by The Human Genome Organisation (HUGO)
• "Literature aliases": other gene symbols used in literatures (known as aliases), see HUGO help
• Ug_id: the UniGene Cluster ID
• Gb_id: the GenBank accession number
• Human and Mouse Cytoband: the cytogenetic location of a gene

2. Enter keyword [next step] [previous step] [top]

• All the search is case insensitive. 
• Partial word is also acceptable. 
• Logic operations "and" and "not" are not available.
• Logic operation "or", i.e. "|", can ONLY be used in "Gene description + Gene name". For example, "smn|eif4g" will find records that contains "smn", or "eif4g", or "smn, eif4g".
• Query against Ug_id must be exact, e.g. "hs.2" or "Hs.2" can only retrieve Hs.2, but not Hs.22, Hs.222, Hs.2222, etc.
• Query against cytogenetic locations
• Human: use the "n[p|q]n" format (e.g. 1p36, 1q20, etc)
• Mouse: e.g. "1 40" means position 40 cM on chromosome #1

3. Set the optional parameters [search results] [previous step] [top]

The default species is human. The search speed will be slowing down by selecting both human and mouse.  In order to perform the AS comparison between human and mouse, users can also use the hyperlinks "homologs" or "similarities" in the graphical output of "AS lists" and "All seq info".

PALS db saves all the predicted AS sites and marked those sites that pass the threshold criteria. The default setting is 95% identity on both ends of alignment at least 50-bp in length (See rationale for details). Hopefully, the users can take advantage of the unmarked information to 

• to enhance the confidence on prediction 
• to recover false negatives

[previous step] [top]

Search Results

The results are displayed in an eight-column table (not the six-cloumn table shown below)

1. Ug_id: The UniGene cluster id will hyperlink to NCBI's UniGene database
   • Green background: UniGene clusters that have at least one predicted AS site at the given threshold in the query interface
   • Gray background: UniGene clusters that don't have any predicted AS site at the given threshold in the query interface
2. Gene: Will hyperlink to alias list of the given gene name
3. UniGene member: List the number of all sequences in a given UniGene cluster
4. AS lists: Will hyperlink to non-redundant AS information in graphics
5. Text Info: Will hyperlink to text information for those UniGene clusters that pass the filtering criteria
6. All seq info: Will hyperlink to a graphical display that have ALL the AS sites regardless of their quality
7. Description: An one-sentence description of a given UniGene cluster
8. Cytoband: List the cytogenetic location of a given UniGene cluster

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Example

Genes with more than 20 putative ASSPs (Release 2, 2001/08/15)

Last updated on 2003-11-01 by Fu, Gloria Chiung-Ling