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ACRE SEA's primary goal is to build capacity within Southeast Asian NMHS to improve and extend historical instrumental, documentary and proxy databases of Southeast Asian weather and climate, in order to contribute to the generation of high-quality, high-resolution historical hydroclimatic reconstructions.
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To perform a replication study of the initial findings, the LD pattern of the 10 SNPs, which showed significance in the Discovery sample, was investigated in the SNAP Proxy database (http://www.broadinstitute.org/mpg/snap/ldsearch.php).org/mpg/snap/ldsearch.php
These proxy reference databases were established as the pea genome is not available and the inclusion of additional ascomycetes genomes to S. sclerotiorum (strain 1980) improved the assignment rate.
Prior research uses CSR performance proxies from databases such as MSCI KLD or Bloomberg (Cho et al. 2013; Nelling and Webb 2008).
For uniformly heterozygous positions, the minor allele was assigned to the paternal and maternal chromosome scaffolds using pair-wise pre-computed population linkage disequilibrium (LD) data from the SNP Annotation and Proxy Search SNAPP) database [ 67].
Only 5.5% of ESTs had zero similarity to either of the proxy-reference genomes, and 4.3% of ESTs had high similarity to both the plant and fungal proxy-reference genome databases (Table 1).
So at MariaDB, the team decided to now license the latest version of its MaxScale database proxy under the BSL (MariaDB itself is a fork of MySQL, so it is forever bound to the open-source GPL license that MySQL is licensed under).
Briefly, the mixed ESTs were compared with tBLASTx (NCBI-BLAST-2.2.24+) to fungal and plant "proxy-reference" genome databases (Table 8).
Using an e-value threshold of 1e-3, 35,688 mixed ESTs from pea and S. sclerotiorum were compared to legume and fungal proxy-reference genome databases and parsed using the tBLASTx program.
However, in pea these resources are not available, therefore, we used a standalone BLAST approach against proxy-reference genome databases with high genetic similarity to pea or S. sclerotiorum to distinguish mixed transcripts.
4,098 ESTs were assigned to pea based on an e-value ratio >1e, 5,649 ESTs were assigned to S. sclerotiorum based on an e-value ratio <1e-20, while 1,519 ESTs were difficult to distinguish due to high e-value alignments to both proxy-reference genome databases, with e-value ratios between 1e-20 and 1e.
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