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AL2CO specifications


Unique identifier OMICS_15454
Name AL2CO
Interface Web user interface
Restrictions to use None
Input data A protein sequence alignment.
Input format CLUSTAL
Programming languages C
Computer skills Basic
Stability Stable
Maintained Yes



  • person_outline Nick Grishin

Publication for AL2CO

AL2CO citations


Structurally distinct Mre11 domains mediate MRX functions in resection, end tethering and DNA damage resistance

Nucleic Acids Res
PMCID: 5888019
PMID: 29420790
DOI: 10.1093/nar/gky086

[…] rposition of Mre11 and Rad50 (ATP-bound) on the tetrameric complex structure from M. jannaschii (PDB ID: 5F3W) (). This structure was then refined by molecular dynamics. A multiple alignment based on AL2CO structural conservation () of ScMre11 with Mre11 orthologs from Homo sapiens (PDB ID:3T1I), Schizosaccharomyces pombe (PDB ID:4FCX), Chaetomium thermophilum (PDB ID:4KYE and 5DA9 for RBD region) […]


LAR RPTP Clustering Is Modulated by Competitive Binding between Synaptic Adhesion Partners and Heparan Sulfate

PMCID: 5645493
PMID: 29081732
DOI: 10.3389/fnmol.2017.00327

[…] 38 on IL1RAPL1 also participate in a broad range of interactions with the PTPδ* Ig3 domain. A sequence conservation analysis was performed on the sequences listed in Supplementary Table S3, using the AL2CO (Pei and Grishin, ; Pettersen et al., ). It showed that the key residues at Interface I and Interface II involved in the lateral interaction are highly conserved (Supplementary Figure S3C). […]


Enter the Dragon: The Dynamic and Multifunctional Evolution of Anguimorpha Lizard Venoms

PMCID: 5577576
PMID: 28783084
DOI: 10.3390/toxins9080242
call_split See protocol

[…] y sequence and with conservation of the cysteine residues. Protein models were rendered in UCSF Chimera version 1.10.2 []. Conservation scores were calculated using the UCSF Chimera implementation of AL2CO under the default settings [,]. Tests for selection were performed using HyPhy version 2.220150316: overall dN/dS value was calculated using the AnalyzeCodonData method, persistent site-by-site […]


When loss of function is loss of function: assessing mutational signatures and impact of loss of function genetic variants

PMCID: 5870554
PMID: 28882004
DOI: 10.1093/bioinformatics/btx272

[…] on features for the wildtype sequence were extracted from two sources. First, we generated a position-specific scoring matrix (PSSM) by running PSI-BLAST against the "nr" database (). Second, we used AL2CO () to derive nine conservation indexes from the UCSC Genome Browser 46-species alignment () for each position in the sequence. Both normalized and unnormalized versions of these scores were calc […]


Protein sites with more coevolutionary connections tend to evolve slower, while more variable protein families acquire higher coevolutionary connections

PMCID: 5506539
PMID: 28751967
DOI: 10.5256/f1000research.12138.r21733
call_split See protocol

[…] Analysis of positional conservation in a sequence alignment can aid in the detection of functionally and/or structurally important residues. The AL2CO program performs conservation analysis in a comprehensive and systematic way. It was used to calculate the conservation index for each position for a given multiple sequence alignment. Twelve d […]


Oncodomains: A protein domain centric framework for analyzing rare variants in tumor samples

PLoS Comput Biol
PMCID: 5398485
PMID: 28426665
DOI: 10.1371/journal.pcbi.1005428

[…] at have known function, functional feature annotations for each protein position were obtained from UniProt on July 18th 2015. To determine the conservation of each domain position j, we employed the AL2CO [] algorithm for assessing entropy via the following formula: Hjh=−∑i=1,20p(ai,j)ln⁡(p(ai,j)) Here, p(ai,j) is the amino acid frequency for amino acid ai at position j and Hj is the AL2CO score […]


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AL2CO institution(s)
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA

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