Because the PTP method requires a correctly rooted tree, we use the following two rooting strategies: if the branch leads to a tip, apart from the query sequences, we extend the alignment by including the reference tree tip sequence and that reference sequence that is furthest away from the current tip.
Apart from simple queries that focus on only one GO term or gene, two types of batch queries are supported: First, different, user-defined GO terms can be simultaneously queried using the GO Slimmer, a method that uses parent-child relationships between GO terms to compare gene lists of interest with lists that are annotated to GO terms.
Apart from posing queries, the audience also shared some relevant suggestions.
RI Dogan, GC Murray, A Névéol and Z Lu [1] established that apart from bibliographic queries (such as author name and article title), chemical entities are some of the terms frequently used to browse and search the PubMed database.
Apart from this, processing queries in a spaced suffix array is similar to what is done with ordinary suffix arrays, a topic we discussed in section 'Query string search'.
Apart from the above mentioned query options, RETINOBASE also provides a user-friendly transcriptomic data visualization tool that was developed to allow retinal biologists to graphically analyse gene expression profiles across all the experiments.
Notes and queries Apart from raising, what are eyebrows for?
Treatment of SH-SY5Y cells with RA resulted in induction of all regions under query with a 3-5-fold magnitude for most of them, apart from the primer pair 5 (Pri_5) querying the first two exons of UCSC LOC401022 isoform starting at the promoter region 1, which was induced only 2-fold.
The Queries were set apart from the main text of the Opticks in order to underwrite their speculative nature.
Apart from providing a wide selection of queries for integrating expression data with gene annotations, CellMiner offers metadata on the cell lines, the profiling platforms, and the profile data sets.
