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The common idea shared by these pipelines is to run an assembler at different k-mer lengths and to merge these assemblies into one.
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In order to test whether the glycosylation status determines the assembly into one particular SPP complex, we analysed OP91H* SPP and OP91H* SPPD/A complexes using 2D-BN-SDS/PAGE.
This is not surprising, as these genes tend to have hypervariable central regions, therefore such low global similarity levels prevent their assembly into one cluster.
In DW7-ToxB, the flanking regions are on two contigs; however, there is a repeat region at the end of one of the contigs that would most likely prevent de novo assembly into one larger contig.
Attempts to solve this fragmentation problem have included combining two types of short read data produced from a Roche 454 and Solexa Illumina [ 36], or utilizing paired-end information; however, assembly into one fully connected scaffold is difficult to achieve.
When co-expressed with SPP or SPPD/A, glycosylated and non-glycosylated OP91H* forms were detected to similar extents in the 200, 400 and 600 kDa complexes, indicating that the glycosylation status does not determine OP91H* assembly into one particular SPP complex.
Sequences of amino acids with high β-sheet propensities promote assembly into one-dimensional nanostructures in water.
Nine assemblies were resolved into one scaffold that contains linkers and spacers as necessary, while BAC31 assembled into two unoriented contigs.
Orthologs identified from ten de novo liver transcriptome assemblies were joined into one 'super gene' for each species.
The resulting two assemblies were combined into one using Cap3 [ 30] at default settings and contigs were labeled by whether they derived from both assemblies (high confidence assembly; highCA), or one assembly only (lowCA; for a detailed analysis of the assembly categories see the supporting Methods file).
We emphasize that due to the presence of repeated sequences such as IS elements hinder the assembly of genomes into one single scaffold.
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