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In conjunction with the homology-based searches, putative gene predictions were assembled together with information from predicted in silico sequences provided by Beebase, albeit the homology-based gene predictions produced sequences with higher sequence identity to characterised vertebrate neuroligin and neurexin genes.
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For in silico MLST prediction, trimmed reads were assembled de novo using Velvet 32 with a k-mer size of 81 and searched using nucleotide BLAST against the multilocus sequence database downloaded from the pubMLST website on 5 August 2013 (http://pubmlst.org/paeruginosa/).org/paeruginosa/
cDNA sequences were assembled using a combination of Ensembl gene predictions and EMBL ESTs as references.
If there were matching ESTs, they were assembled into transcripts, and compared to the predictions, if there were any.
To facilitate the prediction of the miRNA target gene, shrimp ESTs (162,926 EST reads) were assembled.
Images were assembled using Photoshop.
Chromatograms were assembled in DNASTAR Lasergene SeqMan Pro v.7.1.0.
Four transcriptomes were assembled.
92,511 scaffolds were assembled.
The Sf21 genome was assembled using Velvet and gene prediction analysis was performed using Augustus.
This technique was applied to entire protein chains rather than to pieces that must be folded separately before being assembled, reducing the complexity of the prediction process".
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