PFAAT specializes in the annotation and analysis of a MSA, and since the release of version 1.0, we have continued to develop and add novel features to PFAAT. More recently, it has been recognized that MSAs can be used to validate and propagate annotations to other sequences. Additionally, MSA viewers provide various tools for sequence and structural analysis. Alignment editing tools are available in PFAAT as well as several other applications.
BIOEDIT USER MANUAL MANUAL
Alignment accuracy is usually dependent on the percent amino acid identity between sequences and manual editing is often a necessary step.
BIOEDIT USER MANUAL SOFTWARE
There are several excellent software packages that align multiple sequences. Subsequent analysis typically includes phylogenetics, homology modeling, structure prediction, and binding site prediction. The annotations can be combined with sophisticated analysis to test hypothesis that relate to sequence, structure and function.īuilding a multiple sequence alignment (MSA) is a critical step towards understanding the function and evolution of a protein family. PFAAT provides a framework whereby end-users can specify knowledge for a protein family in the form of annotation. Other features include: novel algorithms to compute sequence conservation, mapping conservation scores to a 3D structure in Jmol, displaying secondary structure elements, and sorting sequences by residue composition. Residue annotations are also searchable, and allow one to quickly select alignment columns for further sequence analysis, e.g. Residue annotations are accessible from the alignment viewer and are typically used to designate binding sites or properties for a particular residue. The selected sequences can be further analyzed using statistical methods that explicitly model relationships between the sequence annotations and residue properties. Once a multiple sequence alignment is populated with sequence annotations, sequences can be easily selected and sorted through a sophisticated search dialog. Sequence annotations can be created manually or extracted automatically from UniProt entries. The sequence annotations are accessible from the alignment and tree, where they are typically used to label sequences or hyperlink them to related databases. Support for multiple annotations is a key component of this release as it provides a framework for most of the new functionalities. Here we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. By virtue of their shared ancestry, homologous sequences are similar in their structure and function.
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