SeqFIRE : a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments
(2012) In Nucleic Acids Research 40(Web Server issue). p.7-340- Abstract
Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of... (More)
Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.
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- author
- Ajawatanawong, Pravech ; Atkinson, Gemma C LU ; Watson-Haigh, Nathan S ; Mackenzie, Bryony and Baldauf, Sandra L
- publishing date
- 2012-07
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Algorithms, INDEL Mutation, Internet, Proteins/genetics, Sequence Alignment/methods, Sequence Analysis, Protein, Software
- in
- Nucleic Acids Research
- volume
- 40
- issue
- Web Server issue
- pages
- 7 - 340
- publisher
- Oxford University Press
- external identifiers
-
- scopus:84864446807
- pmid:22693213
- ISSN
- 1362-4962
- DOI
- 10.1093/nar/gks561
- language
- English
- LU publication?
- no
- id
- f827a772-2ff7-4347-a375-aa73b8a0ce34
- date added to LUP
- 2021-09-27 15:55:37
- date last changed
- 2024-01-05 16:41:22
@article{f827a772-2ff7-4347-a375-aa73b8a0ce34,
abstract = {{<p>Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.</p>}},
author = {{Ajawatanawong, Pravech and Atkinson, Gemma C and Watson-Haigh, Nathan S and Mackenzie, Bryony and Baldauf, Sandra L}},
issn = {{1362-4962}},
keywords = {{Algorithms; INDEL Mutation; Internet; Proteins/genetics; Sequence Alignment/methods; Sequence Analysis, Protein; Software}},
language = {{eng}},
number = {{Web Server issue}},
pages = {{7--340}},
publisher = {{Oxford University Press}},
series = {{Nucleic Acids Research}},
title = {{SeqFIRE : a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments}},
url = {{http://dx.doi.org/10.1093/nar/gks561}},
doi = {{10.1093/nar/gks561}},
volume = {{40}},
year = {{2012}},
}