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Text Information of AS
Contents
Aim
Graphic presentation can convey lots of information in a small area, so it is a great tool to present a global view. However, it is difficult to get precise position from a graph. For example, the length of matches can be estimated from the scale bar, but it is not precise. All the candidate sequences containing alternative splicing information are clustered into an alternative splicing site pair (ASSP). The Text information complements the nature of a graphic presentation. Moreover, text information of PALS db is formatted and it should be quite easy to import into an Excel table for further analysis.
Abbreviations
- Each ASSP record has 5 components
- [n]: the first line of a ASSP record in this given gene
- ALTER_INFO: general information about an ASSP
- AS_SEQ_COUNT: the number of supporting evidences from different sequence sources.
- AS_SEQ_INFO: such as accession number, etc.
- LIB_INFO: the cloning library information
- Other features
- [n]**: the records that are above threshold set by the users. In the above example, it is more than 95% identity in a minimum of 50 bp alignment.
- Here are the explanation of abbreviations:
AS alternative splicing ASSP alternative splicing site pair ug_id The UniGene Cluster ID of a unique gene ref_unigene_id The UniGene accession number of the reference sequence used to collect AS information in PALS db ref_gb_id The GenBank accession number of the reference sequence ref_len The length of the reference seqeunce ALTER_INFO POS1=708 POS2=997 The un-aligned starts at POS1 and ends at POS2. For AS type II, POS2 would be 0 because the un-aligned fragment is on the target sequence, not the reference sequence. ID1=97 ID2=93 The quality of both ends of alignments between the reference sequence and the candidate AS sequence. ID means identity of alignment. LEN1=212 LEN2=63 The length of both ends of alignments. VARIANT_SIZE=288 The length change of this ASSP. For AS type I, this means that candidate AS sequences may lack a fragment of this length. For AS type II, this means that candidate sequence contains an addition fragment of this length. ALTERTYPE=1 The type of AS is "I" [1] [2] ... The serial number of ASSPs for this gene AS_SEQ_COUNT CDS_C=0 The number of coding sequences supporting this ASSP C_CDS_C=0 The number of complete coding sequences C_SEQ_C=0 The number of complete sequences S_EST_C=1 The number of EST sequences from this UniGene (self) cluster O_EST_C=0 The number of EST sequences from other UniGene cluster (paralogous gene) DB_EST_C=0 The number of EST sequences from non-clustered EST sequences (dbEST) AS_SEQ_INFO AW407628 The GenBank accession number of sequences supporting this ASSP SelfClusterEST Tthe source of the sequence containing AS information
Other values can be OtherClusterEST, and CDS.LIB_INFO LIB=NIH_MGC_38 The cloning library title of the EST sequence TISSUE=pooled tissue The tissue type of the library HISTOLOGY=normal The histology of the library, other values can be cancer, pre-cancer, etc. CELL_TYPE=flow-sorted The cell type of the library, other values can be bulk, microdissection, etc.