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gambiae H1 candidate proteins (XP_311486) to a histone H1 protein from C. thummi, and examined the alignment for precise matches (Fig. 1A) that did not match well in a separate alignment of the An.
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In addition to the full protein alignments, we built a separate alignment for PDZ domains (as in ref [ 2] but with an extended gene sampling) and constructed specific alignments for the SAM and SH3 domains of Shank.
A separate alignment was then edited manually for each allele.
The separate alignment option aligns all sequences against different references separately in a run.
In the next step, the initially obtained 1,634 candidate contigs were split into batches of 150 sequences and each batch was also added to the master alignment using MAFFT (-add option) resulting in 11 separate alignments.
The V regions of syndecan-3s are well-conserved between fish, chicken, mouse and human, yet the V region of the Xenopus syndecan-3s have unique features that result in a separate clustering in the sequence alignment.
Secondary structures for resulting clades were established for certain representatives of the clade by aligning to known structures from the European RNA Database [ 18, 33] in separate alignments for each clade and considering compensatory base changes.
In order to align the virus-labeled bouton profiles with the data on soma distributions and dendritic labelings from different experiments, we defined landmarks in each of the experiments (the details of alignment are described in a separate section, see below).
Each alignment will be stored in a separate file.
MGAviewer is already adopted by CAMERA project in its alignment resources, which will be described in a separate publication.
The alignment of the classification of the GO with the ChEBI roles will be undertaken in a separate project.
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