Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features
By Timo Lassmann, Oliver Frings, Erik L. L. Sonnhammer. Nucleic Acids Research, 2008
295 citations recorded by the source corpus.
In the growing field of genomics, multiple alignment programs are confronted with ever increasing amounts of data. To address this growing issue we have dramatically improved the running time and memory requirement of Kalign, while maintaining its high alignment accuracy. Kalign version 2 also supports nucleotide alignment, and a newly introduced extension allows for external sequence annotation to be included into the alignment procedure. We demonstrate that Kalign2 is exceptionally fast and memory-efficient, permitting accurate alignment of very large numbers of sequences. The accuracy of Kalign2 compares well to the best methods in the case of protein alignments while its accuracy on nucleotide alignments is generally superior. In addition, we demonstrate the potential of using known or predicted sequence annotation to improve the alignment accuracy. Kalign2 is freely available for download from the Kalign web site (http://msa.sbc.su.se/).
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/7902c0b4d2cd41866656ad7d811e42aa6f50106b
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Citations in the corpus
- Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals (2010, methodology): “to reduce the number of sequences used in the multiple alignment. These clusters were annotated by the number of reads in each sample and then aligned using KALIGN”
- CASP8 results in context of previous experiments (2009, methodology): “%) from CASP5.”
- The EMBL-EBI bioinformatics web and programmatic tools framework (2015, methodology): “In 2009 the Job Dispatcher framework (2,3) was released to provide consistent, robust and updat-able access to modern bioinformatics tools such as NCBI BLAST+ (4) and PSI-Search (5) for sequence similarity searching; InterProScan (6) and PfamScan (7) for protein functional analysis; and multiple seq”
- OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization (2023, unknown): “OpenFold immediately makes possible two broad areas of advances: (1) deeper analyses of the strengths, weaknesses and learning behavior of AlphaFold2-like models and (2) development of new (bio)molecular models that take advantage of AlphaFold2 modules.”
- InParanoid 7: new algorithms and tools for eukaryotic orthology analysis (2009, methodology): “A multiple sequence alignment can be viewed in Kalignvu (37) or downloaded in various formats such as FASTA, Stockholm, MSF or SELEX.”