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The amino acid sequence alignment of Group 1 LILRs also predicts that LILRA3 recognizes classical HLAIs less well than LILRA1, LILRB1, and B2, as well as that LILRA3 may recognize the fHCs of classical HLAIs.
SPADA was run with an e-value of 0.1 on all available plant genomes (Table 1) using an HMM profile based on the multiple sequence alignment of group 567 from Graham et al. (2004).
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Phylo is a game in which the four bases in DNA are represented by blocks of different colour: the aim of the game is to move groups of blocks to the left and right in order to find the best possible alignment of groups with each other.
Alignment of groups of novel, peripheral, environmental sequences thus revealed by network analyses can guide the design of new sets of primers which will be useful to expand our knowledge of microbial diversity, moving it further away from the current status quo and its logical starting point: the sequences of cultured organisms.
For these groups, we inspected an alignment of the group, selected a representative member, and included that in the database.
The resulting alignments of groups I to VI are available as FASTA format files (see Additional file 4; Additional file 5; Additional file 6; Additional file 7; Additional file 8; Additional file 9).
Marker annotation with rainbow trout linkage group name permitted alignment of linkage groups between the two species and inference of Chinook linkage group structure.
A 440-bp consensus nt sequence of the group 1 CoV was obtained on the basis of alignment of 4 group 1 CoV sequences detected (>98% nt identity with each other) and deposited in GenBank as Bat-CoV/Philippines/Diliman1552G1/2008 (DNA Database of Japan [DDBJ] accession no. AB539080).
The location of the insertion as seen in these comparisons is the same as that seen in the alignment of a Group I nitrogenase, such as A. vinelandii NifD with C. kluyveri NifD.
The primers, listed in the legend to Table 1, were designed using the full-length genome alignment of diverse group M HIV-1 strains from the HIV sequence database [2].
A tile is defined as the alignment of one group of ordered residues on the subject sequence with a partition of ordered residues on the query sequence.
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