ArticleAlgorithms for molecular biology : AMB2006
Multiple sequence alignment with user-defined anchor points.
Article in Algorithms for molecular biology : AMB, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- Leveraging protein language models for accurate multiple sequence alignments.Genome research · 2023Article
- Article
- Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors.PloS one · 2021Article
- In silico structural elucidation of RNA-dependent RNA polymerase towards the identification of potential Crimean-Congo Hemorrhagic Fever Virus inhibitors.Scientific reports · 2019Article
- Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points.Bioinformatics (Oxford, England) · 2019Article
- Caenorhabditis elegans DAF-2 as a Model for Human Insulin Receptoropathies.G3 (Bethesda, Md.) · 2017Article
- DIALIGN at GOBICS--multiple sequence alignment using various sources of external information.Nucleic acids research · 2013Article
- A lossy compression technique enabling duplication-aware sequence alignment.Evolutionary bioinformatics online · 2012Article
- Article
- ABC transporters coordinately expressed during lignification of Arabidopsis stems include a set of ABCBs associated with auxin transport.Journal of experimental botany · 2011Article
- A monte carlo method for assessing the quality of duplication-aware alignment algorithms.Evolutionary bioinformatics online · 2011Article
- Automatic detection of anchor points for multiple sequence alignment.BMC bioinformatics · 2010Article
- MS4--Multi-Scale Selector of Sequence Signatures: an alignment-free method for classification of biological sequences.BMC bioinformatics · 2010Article
- DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS.Nucleic acids research · 2010Article
- OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.BMC bioinformatics · 2009Article
- Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family.Algorithms for molecular biology : AMB · 2008Article
- DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment.Algorithms for molecular biology : AMB · 2008Article
- Genomic evolution of the proteasome system among hemiascomycetous yeasts.Journal of molecular evolution · 2007Article
- RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints.Nucleic acids research · 2007Article
- G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis.The Plant cell · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAutomated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments.
resultsHerein, we describe a semi-automatic version of the alignment program DIALIGN that can take pre-defined constraints into account. It is possible for the user to specify parts of the sequences that are assumed to be homologous and should therefore be aligned to each other. Our software program can use these sites as anchor points by creating a multiple alignment respecting these constraints. This way, our alignment method can produce alignments that are biologically more meaningful than alignments produced by fully automated procedures. As a demonstration of how our method works, we apply our approach to genomic sequences around the Hox gene cluster and to a set of DNA-binding proteins. As a by-product, we obtain insights about the performance of the greedy algorithm that our program uses for multiple alignment and about the underlying objective function. This information will be useful for the further development of DIALIGN. The described alignment approach has been integrated into the TRACKER software system.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.