Protein Sequence Alignment for Two Protein SequencesNan Xiao
As such, PSI-BLAST identifies hidden conservation patterns characteristic to a given protein family that cannot be detected by BLAST. Indeed, PSI-BLAST identified stronger conservation patterns between sequences encoding HTH4 and wH folds. This alignment approach also shifted the alignment registers of...
Two amino acid sequence alignments of BgxA, based on its same family enzymes' alignment and conserved domain alignment from NCBI, were used to select the suitable residues for mutations and substitutions, respectively. Upon selected 9 single mutants, Q290E and Q421L showed a 1.5 to 1.7-fold ...
Two-Level Protein Methylation Prediction using structure model-based features Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments . Bioinformatics 2006; 22 :1536-7; PMID:16632492; http://dx.doi.org/10.1093/bioinformatics/btl151 [ Cross Ref ]... ...
The ratio of synonymous (dS) to nonsynonymous (dN) sites was calculated for each pair of Lh–Lb orthologs as follows: based on the multiple alignment of protein sequences by MUSCLE v3.8.386, Pal2Nal v13 was used to retrieve the corresponding CDS data; the CodeML module of the PAML ...
As shown in the protein sequence alignment, the first half (1–220 aa) of the trout myomaker protein sequence was well-conserved, sharing 88 and 71% identity with the zebrafish and mouse myomaker proteins, respectively. An analysis of the amino acid sequence showed that the two cysteines ...
Figure 1. Protein sequence alignment and expression of BNGR-A25S, -A25L, and -A27 in HEK293 and Sf21 cells. A, protein sequence alignment of BNGR-A25S (accession number AB330446), BNGR-A25L, and BNGR-A27 (accession number AB330448) with CAPA receptors from D. melanogaster (Dme-Capa...
consistent with their poor whole-genome sequence alignment. We found that CaT2T centromeres (Fig.3aand Supplementary Figs.16and17) and telomeres (Fig.3b) exhibited active transcription of both transposons and protein-coding genes, as suggested by RNA-seq analysis. For example, approximately 42 (...
format the peptide-protein data like (protein sequence, peptide sequence, protein_ss, peptide_ss) and generate a test data file called "test_filename" for Use the commandpython -u preprocess_features.py test_filenameto obtain processed feature dicts in ./preprocessing/ ...
in buffer C (buffer A containing 70 mM NaCl). The hTop2βcoreprotein (with molecular weight about 180 kDa) was collected and concentrated to 6.5 mg/ml for crystallization. DNA substrate for crystallography The DNA sequence 5′-AGCCGAGCTGCAGCTCGGCT-3′ of the double-stranded DNA sub...