[Introduction] [Rationale] [History]
[User's Guide] [AS Lists] [Text Info] [All Seq Info] [Hyperlinks] [Related db]
All Candidate Sequences Containing Putative AS
Contents
Aims
- To display the detailed information about each predicted ASSP.
- To provide users the flexibility of judging the quality and validility of each candidate AS-containing sequence by visualization.
- To provide users the information of tissues, histology, and sampling protocols related to the candidate AS-containing sequences.
Symbols
- (aa) and (nt)
(aa): sequence scale in unit of amino acid position
(nt): sequence scale in unit of nucleic acid position - gb_id
GenBank accession number of the sequence - seqtype: the sequence type (EST, cds, etc.)
OCls EST from Other UniGene Cluster, Cds coding seqeunce, Ccds complete coding sequence, SCls EST from this (Self) UniGene Cluster dbEST EST not clustered to any UniGene Cluster (new EST in dbEST) - rel_ug
The (real) UniGene cluster ID (by NCBI UniGene clustering) of the sequence - "*"
Indicates that an AS candidate passes the optional criteria selected by this query. The threshold used in the above figure was the default. The default threshold is 95% identity and 50-bp alignment on either ends of an ASSP. For further information about the criteria, refer to rationale. - (is=)
The insert size of a type II candidate AS
Features
- Designed to recover the false negatives: We have used a stringent criteria to create the
statistics; however, this criteria may miss some real signal. A graphic interface will
allow the user to identify false negatives interactively.
- Quality of alignment is indicated by different colors:
- Red: 95 - 100 % identity
- Pink: 90 - 94 % identity
- Green: 85 - 89 % identity
- Blue: 80 - 84 % identity
- Black: less than 85 % identity
- The length of matched region can be measured in units of either amino acid position or nucleotide position on the scale bar
- The symbol "*" indicates those EST sequences that pass the threshold set in the "optional parameters" of the query interface
- The supporting ESTs are shown by clustering those EST sequences that have identical ASSPs
- Quality of alignment is indicated by different colors:
- Designed to reveal the effect of alternative splicing on proteins
- Coding region of the reference sequence is shaded by pale blue color
- Sequence scales using both amino acid and nucleic acid positions
- Hyperlink to InterPro, CDD, DART will reveal the positions of protein signatures, motifs, and domains
- Designed to display the detail information about a given EST
- Each EST sequence is hyperlinked to GenBank and UniGene
- "MouseOver" each EST for two seconds will display the library information (tissue origin) in the message line
- Designed to display other useful information to compare with alternative splicing information