Sentence examples for splice file from inspiring English sources
With the information in the splice file, the program can accurately anchor the vector sequence around the vector-insert border onto the ESTs in test.
However, preparation of an accurate splice file is heavily reliant on users' thorough understanding of the cloning history and careful drafting of the border sequences.
A splice file contains two pairs of sequences: up to 150 base long sequences upstream or downstream of the cloning site on the vector in either orientation.
The problem with SeqClean did not appear to exist in LUCY2 (Table 3), possibly due to the design of a user-provided splice file required by the program which specified the 100 to 150 bp vector sequences upstream or downstream of the ligation site.
For the LUCY2 trimming, in addition to files of EST or vector sequences, splice files were prepared as input data.
Two splice files were prepared for each cloning vector, one for CVS and the other for RVS.
The sequences in the splice files made from CVS or RVS of one cloning vector were basically identical except that the extended lengths derived from pDNR-LIB, pGEM-Teasy and pT7Blue were a little shorter for CVS than RVS since their splice sites fall within 100 bases from the start points of the vector sequences.
This splice junction file was then with a list of all possible junctions between the annotated 5′ and 3′ splice sites of isoforms in the annotation (to detect novel alternative splicing).
Finally, we observed that methylated honeybee genes that are also alternatively spliced were even higher conserved across species than methylated genes that were not alternatively spliced (Additional file 1: Table S1) or than alternatively spliced genes that are not methylated (Additional file 1: Table S2).
For analysis of splicing differences, the file splicing.diff output by cuffdiff was used.
The splice junction files contain both novel and annotated splice junctions based on the 8-track annotation file, which can be parsed to identify each of the novel features.
