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These markers were projected onto the reference Vitis map by map alignment with common markers, and are reported underlined and in italics [see Additional file 2].
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First, for a given view, all 3D markers are projected onto the corresponding image (b), and those affected by body auto-occlusions are removed (c).
Marker positions were projected on the Vitis reference map by map alignment using common markers.
To determine the relative physical positions of the SSR markers, their primer sequences were projected over a reference rice genome (e; Jeung et al.2007), Os-Nipponbare-Reference-IRGSP-1.0 (http://rapdb.dna.affrc.go.jp%/download/irgsp1.html), using the 'BLAST' menu at the Rice Annotation Project database (RAP-DB) (http://rapdb.dna.affrc.go.jp/tools/blast).jp/tools/blast
The rice genetic linkage map of Temnykh et al. [ 19] was used as a reference map, on which the markers of 15 studies were projected to develop a consensus map.
To facilitate the visualization of the QTLs and meta-QTLs and the shift back to markers, the QTLs and meta-QTLs were projected on a virtual physical map composed of microsatellite markers corresponding to those used to build the IR64xAzucena SSD genetic map (Ahmadi et al., unpublished data).
On the contrary, bone marker changes affected through GnRH inhibition were projected to change too slowly to provide reliable dose differentiation; for example, these markers would likely require at least 3 months to show marked differences.
QTL intervals were projected on the physical genome sequence by anchored markers (flanking SSRs).
QTL were projected on the reference genome sequence of P. trichocarpa, using anchored markers.
Among those, 334 SSR/STS and 623 DArT markers could be projected onto the consensus linkage map and were used for LD and marker-phenotype association tests (957 markers).
The final integrated marker order was projected onto a common relative scale representing all markers.
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