Sentence examples for database cut off from inspiring English sources

Note: Blast run against NCBI NR database, cut off 1e-05 Numbers in parentheses represent the number of oligos that match a particular gene that was upregulated.

Only 12 of the remaining 7,057 alfalfa sequences without a match in any of the aforementioned databases had a hit in the Arabidopsis TAIR 9.0 protein database (cut off E value 1e-5).

The absence of introns in the ESTs, a higher level of conservation expected at protein level and use of a different mining criterion, resulted in an increased proportion of reads (30.9%) having significant hits against the nr protein database (cut off E = e-5), though this only represents the similarity to known proteins in other organisms.

The non-redundant sequences were assigned HomoloGene IDs based on the best Blast matches to the database (minimum cut off = E-value < 1 × 10-5).

The "MATCH" program [ 52] was used to identify potential transcription factor binding sites in the 5000 bp preceding the 5' UTR, using the Vertebrate matrix of the TRANSFAC 5.0 database, with cut off values set to "minimize false positives and false negatives".

Parallel searches with BLASTX and BLASTN were performed against the non-redundant database (e value cut off of 1e-4) andatabasebase of Citrus ESTs from GenBank (e value cut off of 1e-15), respectively.

L. rhinocerotis gene models were aligned to fungi P450 sequences and the detected CYPs were named according to nomenclature in the P450 database (cut-off e-value ≤ 1e-10, identity > 30%) at Cytochrome P450 homepage (http://drnelson.uthsc.edu/CytochromeP450.html) [ 22].

To begin with using BLASTX and BLASTN, the assembled sequences were searched against the Nr, Swiss-Prot protein databases and Nt nucleotides database (cut-off E-value of 1e−6).

First, all sequences were subjected to blastx (basic local alignment tool) searches against the National Center for Bioinformatics (NCBI) sequence database with E-value cut off of 10^-3.

The user progresses through a series of menus, selecting fasta file name, database name, E-value cut off and number of top hits.

A BLAST search of all contigs in the high coverage dataset (7,325 sequences) produced 3,788 positive hits (BLASTx search of the NCBI nr database, minimum e-value cut off = 10-6; average e-value = 3.4 × 10-9; Additional file 2).