Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees

Enormous databases of short-read RNA-seq sequencing experiments such as the NIH Sequencing Read Archive (SRA) are now available. These databases could answer many questions about the condition-specific expression or population variation, and this resource is only going to grow over time. However, these collections remain difficult to use due to the inability to search for a particular expressed sequence. While some progress has been made on this problem, it is still not feasible to search collections of hundreds of terabytes of short-read sequencing experiments. We introduce an indexing scheme called Split Sequence Bloom Tree (SSBT) to support sequence-based querying of terabyte-scale collections of thousands of short-read sequencing experiments. SSBT is an improvement over the SBT [1] data structure for the same task. We apply SSBT to the problem of finding conditions under which query transcripts are expressed. Our experiments are conducted on a set of 2,652 publicly available RNA-seq experiments contained in the NIH for the breast, blood, and brain tissues. We demonstrate that this SSBT index can be queried for a 1000 nt sequence in under 4 minutes using a single thread and can be stored in just 39 GB, a five-fold improvement in search and storage costs compared to SBT. We further report that SSBT can be further optimized by pre-loading the entire index to accomplish the same search in 30 seconds.

On the number of terms in the middle of almost split sequences over cycle-finite artin algebras

We prove that the number of terms in the middle of an almost split sequence in the module category of a cycle-finite artin algebra is bounded by 5.

EXISTENCE OF ALMOST SPLIT SEQUENCES VIA REGULAR SEQUENCES

Let $(R, \mathfrak{m})$ be a Cohen–Macaulay complete local ring. We will apply an inductive argument to show that for every nonprojective locally projective maximal Cohen–Macaulay object $ \mathcal{X} $ of the morphism category of $R$ with local endomorphism ring, there exists an almost split sequence ending in $ \mathcal{X} $. Regular sequences are exploited to reduce the Krull dimension of $R$ on which the inductive argument is established. Moreover, the Auslander–Reiten translate of certain objects is described.