Multiple alignment, performing

Another alternative is to compute an alignment of the predicted MFE structures. The RNAf or ester program is a new tool to perform such structure alignments and can also construct multiple alignments (in contrast to KNAdistance above). It is available as a web service at http / /bibiserv. techfak. uni-bielefeld.de/rna-forester/ although it does not yet offer multiple alignments. 

Protein (amino acid) sequences are available from databases such as SwissProt/ Trembl or Protein Data Bank (PDB). Most useful is the ability of such databases to perform alignments, the comparison between different sequences. Simple alignment compares two sequences, multiple alignment more than two. 

Retrieve DNA encoding human alcohol dehydrogenase isozymes in fasta format and perform multiple alignment with ClustalW. 

Retrieve amino acid sequences (in fasta format) of human alcohol dehydrogenase isozymes and perform multiple alignment with ClustalW to evaluate their homology. Identify the amino acid substitutions among the seven isozymes. 

Figure 12.18. Output of Pfam search results. Pfam search is performed with amino acid sequence derived from lipoamide dehydrogenase (Schizosaccharomyces pombe). The table for the trusted matches from Pfam-A for pyr redox (pyridine nucleotide disulfide oxidoreductase) and pyr redox dim (pyridine nucleotide disulfide oxidoreductase, dimerization) domains and their alignments (partial) to HMMs ( ->) are shown. The trusted matches from Pfam-B, the potential matches (Thi4 for thiamine biosynthetic enzyme domain), and the bead-on-a-string sketches are not shown. Select the linked domain name to view the functional description of the domain. The HMM alignments are followed by an option button (Align to seed or Align to family) that enables the user to view/save the multiple alignment of each matched family.

Sequence analysis. The GenBank database was searched using the NCBI BLAST program. Consensus sequences were generated and analysed using the programs of the DNASTAR. Multiple alignments of nucleotide were performed with the Clustal... 

Fig. 3. Phylogenetic analysis of acyltransferases. Phylogenetic tree of amino acid sequences of acyl-transferase domains from actinomycete type I PKSs, Multiple alignment and phylogenetic analysis using the bootstrapping method were performed by using CLUSTALW. AVE, avermectin PKS module ERY, erythromycin PKS module FKB, FK520 PKS module MEG, megalomicin PKS module NID, nidda-mycin PKS module NYS, nystatin PKS module OEM, oligomycin PKS module PIK, pikromycin PKS module RAP, rapamycin PKS module RIF, rifamycin PKS module TYL, tylosin PKS module.

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