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These proteins (including paralogs of yeast RAD23 and DSK2) were manually edited from the list of ubiquitin/UBLps for all the organisms investigated.
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Sequence motifs were excised from the multiple sequence alignments, manually edited for insertions or gaps.
While the surface reconstructions were visually inspected, the surfaces were not manually edited, for two reasons.
Each of the masks was manually edited for any miscoverage.
Figures were manually edited for readability using Adobe Illustrator.
The average number of clones recognized by a single probe was 6.9, in good accordance with the assessment of the library redundancy based on the average insert size. 1 mm5 assembly, UCSC To characterize the inserts of the PWD/Ph BAC library at the DNA sequence level we sequenced and manually edited 87 BAC ends from 47 BAC clones (total 38,339 nucleotides).
Multiple alignments were carried out using MUSCLE [45] and manually edited using the program ED from the MUST package [46].
This volume was then thresholded and manually edited to separate white matter from other tissue classes.
CD34 positive blood vessels within a manually edited buffer of 300 μm from any tumor cell in all directions were identified and individually quantified for each sample.
The nucleotide and subsequent protein MSAs were manually edited by removing ambiguous regions from the alignment using the sequence alignment editor, Se-Al 2.0a11 [ 59].
For all of the 223 differentially expressed genes in total, in complement to the information available at the genome browser, we manually edited some of the gene models from the genome browser to get the putative full length gene model, and further searched for InterPro domains (see Materials and Methods and Supplementary Table S2).
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