ProbCons statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ProbCons
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Tool usage distribution map

This map represents all the scientific publications referring to ProbCons per scientific context
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Associated diseases

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Popular tool citations

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Protocols

ProbCons specifications

Information


Unique identifier OMICS_00986
Name ProbCons
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/ProbCons

Documentation


Maintainers


  • person_outline Chuong Do
  • person_outline Mahathi Mahabhashyam

Information


Unique identifier OMICS_00986
Name ProbCons
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.12
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Chuong Do
  • person_outline Mahathi Mahabhashyam

Publication for ProbCons

ProbCons citations

 (189)
library_books

High quality draft genome sequences of Mycoplasma agassizii strains PS6T and 723 isolated from Gopherus tortoises with upper respiratory tract disease

2018
Stand Genomic Sci
PMCID: 5921776
PMID: 29725499
DOI: 10.1186/s40793-018-0315-1

[…] approach (based on BLASTP searches, E-value ≤10− 10) identified 828 pairs of putative orthologs within both genomes. The sequences of proteins encoded by pairs of orthologous genes were aligned using ProbCons version 1.12 [], and were 93.57% identical on average (median: 96.84%). In contrast, comparison of the genomes of M. agassizii strain PS6T and M. testudineum strain BH29T [] revealed much les […]

library_books

Unifying the global phylogeny and environmental distribution of ammonia oxidising archaea based on amoA genes

2018
Nat Commun
PMCID: 5904100
PMID: 29666365
DOI: 10.1038/s41467-018-03861-1

[…] and different length among proteins, sequences of each subunit were separately aligned with 14 different methods: L-INS-i, E-INS-i and G-INS-i strategies of MAFFT v7; PSI-Coffee, EXPRESSO; T-Coffee; ProbCons v1.12; Probalign v1.3; Prank; Muscle v3.7; MSAProbs v0.9.7; Kalign; Dialign-TX; and Clustal Omega. The 10 best alignments were selected after evaluation with MUMSA based on multiple overlap ( […]

library_books

Molecular evolution of DNMT1 in vertebrates: Duplications in marsupials followed by positive selection

2018
PLoS One
PMCID: 5886458
PMID: 29621315
DOI: 10.1371/journal.pone.0195162

[…] The CDSs of human, wallaby, koala, Tasmanian devil, opossum and platypus were translated in silico into protein sequences. The protein sequences were aligned using ProbCons version 1.12 [], and the resulting sequences were used to guide the alignment of the CDSs. Alignments were visualized and, where necessary, manually edited using BioEdit version 7.2.5 []. A p […]

library_books

Novel ATP cone driven allosteric regulation of ribonucleotide reductase via the radical generating subunit

2018
eLife
PMCID: 5794259
PMID: 29388911
DOI: 10.7554/eLife.31529.023

[…] file: PF03477 (). Sequences representing the diversity of NrdB were selected by clustering all NrdB sequences from RefSeq at an identity threshold of 70% using VSEARCH (). Sequences were aligned with ProbCons () and reliable positions for phylogenetic reconstruction were manually selected. A maximum likelihood phylogeny was estimated with FastTree 2 (). […]

library_books

Phylogenetic Distribution of CMP Neu5Ac Hydroxylase (CMAH), the Enzyme Synthetizing the Proinflammatory Human Xenoantigen Neu5Gc

2017
Genome Biol Evol
PMCID: 5767959
PMID: 29206915
DOI: 10.1093/gbe/evx251

[…] re known to be subjected to high rates of error (; ). For each CMAH homolog, the nucleotide sequence of the coding region (CDS) was translated in silico and aligned with the chimpanzee sequence using ProbCons, version 1.12 (). The resulting protein sequence alignment was used to guide the alignment of the CDSs. The CDS alignments were visualized using BioEdit, version 7.0.0 (). Where possible, all […]

library_books

Comprehensive Genome Wide Classification Reveals That Many Plant Specific Transcription Factors Evolved in Streptophyte Algae

2017
Genome Biol Evol
PMCID: 5737466
PMID: 29216360
DOI: 10.1093/gbe/evx258

[…] columns, the longer one was selected.If no suitable alignment could be generated, muscle v3.8.31 was run with two iterations and trimal applied. If that did not lead to a suitable trimmed alignment, ProbCons v1.12 () was applied for alignments of up to 2, 100 input sequences. If that failed as well, muscle was applied with 16 iterations. In cases where trimAl produced empty/too short alignments, […]


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ProbCons institution(s)
Department of Computer Science, Stanford University, Stanford, CA, USA
ProbCons funding source(s)
Supported by an NSF Graduate Fellowship.

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