alternate splicing event determination

Question

[blooming.daisy333]

hi all,

i ve used ASTALAVASTA software to determine alternate splicing events and have following output:

chr1    Undefined   as_event    1871874 1873243 .   +   .   transcript_id "STRG.79.1/STRG.79.2,STRG.79.3"    gene_id "chr1:1868804-1873243W"     flanks "1871874-,null"  structure "1^3-4],2]"   splice_chain "1872150^1873095-1873243],1872197]"    sources "Undefined,Undefined"   NMorMRNA "null"     degree "4"  dimension "2_2"    

chr1    Undefined   as_event    1886878 1887691 .   +   .   transcript_id "STRG.81.1,STRG.81.2"  gene_id "chr1:1884860-1891139W"     flanks "1886878^,1887691^"  structure "1-,2-"   splice_chain "1887614-,1887619-"    sources "Undefined,Undefined"   NMorMRNA "null"     degree "4"  dimension "2_2"

chr1    Undefined   as_event    2119498 2121140 .   +   .   transcript_id "STRG.98.1,STRG.98.2"  gene_id "chr1:2118059-2121140W"     flanks "2119498-,null"  structure "1^3-4^5-6],2]"   splice_chain "2119561^2119968-2120288^2120951-2121140],2119570]"    sources "Undefined,Undefined"   NMorMRNA "null"     degree "4"  dimension "2_2"    

chr1    Undefined   as_event    2381238 2381766 .   +   .   transcript_id "STRG.120.2,STRG.120.1"    gene_id "chr1:2380953-2383475W"     flanks "2381238^,2381766-"  structure "0,1-2^"  splice_chain ",2381490-2381595^"    sources "Undefined,Undefined"   NMorMRNA "null"     degree "4"  dimension "2_2"

my question is that it is easy to classify the result of second and fourth line however i could ot understand what does it mean of the [ ] in the following results "1^3-4^5-6],2]" and "1^3-4],2]" and how they are classified???

waiting for the kind help

many thanks

Answer 1

[328558608]

Splicing sites can be of the following types: 1 Acceptor site (symbol: -); 2 Donor site (symbol:^); 3 Transcription start site (symbol: [); 4 Transcription end site (symbol:]). Excerpt from R package: SplicingGraphs manual pdf

[blooming.daisy333]

thanks for the kind help.

can you plz send me the link. im unable to find it....

Answer 2

[328558608]

sorry I can't add reply directly，maybe caused by my network. Here is the link: http://www.bioconductor.org/packages/release/bioc/html/SplicingGraphs.html Please check the Reference Manual PDF .