ProbCons protocols

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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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Documentation


Maintainers


  • person_outline Chuong Do <>
  • person_outline Mahathi Mahabhashyam <>

Publication for ProbCons

ProbCons in pipelines

 (16)
2018
PMCID: 5794259
PMID: 29388911
DOI: 10.7554/eLife.31529.023

[…] 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 ()., isothermal titration calorimetry (itc) […]

2017
PMCID: 5633207
PMID: 28953979
DOI: 10.1371/journal.ppat.1006589

[…] paracoccidioides brasiliensis pb03 (gca_000150475.2) and pb18 (gca_000150735.2); and emmonsia crescens uamh 3008 (gca_001008285.1). the inferred protein sequences were aligned with probcons [], and alignments were formatted with jalview []., four-day hc cultures were collected and yeast were pelleted by centrifugation. the supernatants were sterile-filtered through 0.22μm […]

2017
PMCID: 5823240
PMID: 28992183
DOI: 10.1093/jmcb/mjx024

[…] factor receptor domain’, ‘kazal-type serine protease inhibitor’, ‘trypsin-like serine protease’, and ‘pdz domain-like’ families, respectively., a multiple sequence alignment was generated using probcons (). this was used with mrbayes () to generate a phylogenetic tree, using a mixed amino acid model and a 4-category gamma distribution with invariant sites. using markov chain monte carlo, […]

2015
PMCID: 4373515
PMID: 25881070
DOI: 10.1186/s12879-015-0870-7

[…] those of a. calcoaceticus xm1570 to generate core conserved proteins, which were defined with a minimum of 95% identity and coverage. those conserved proteins were then concatenated and aligned by probcons with default options []. phyml 3.0 [] was used to construct the phylogenetic tree using the maximum-likelihood method. the tree was bootstrapped 1000 times to estimate the confidence of tree […]

2015
PMCID: 4597091
PMID: 26320580
DOI: 10.1016/j.str.2015.07.016

[…] ha and hb (residues 226–285), which are only present in a subset of the prokaryotic pot family transporters, were removed prior to the sequence alignment. initial alignment was generated using probcons (), and this was manually refined in jalview () to correctly align the functionally important residues identified previously through functional studies on the eukaryotic and mammalian […]


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ProbCons in publications

 (129)
PMCID: 5921776
PMID: 29725499
DOI: 10.1186/s40793-018-0315-1

[…] (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 […]

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 […]

PMCID: 5767959
PMID: 29206915
DOI: 10.1093/gbe/evx251

[…] 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, […]

PMCID: 5737466
PMID: 29216360
DOI: 10.1093/gbe/evx258

[…] 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, […]

PMCID: 5689173
PMID: 29145803
DOI: 10.1186/s12864-017-4242-0

[…] protein fragments when a protein is split due to a frameshift or other mechanisms was set to 1.33 as recommended by the authors. amino-acid sequences of ortholog families were then aligned using probcons, version 1.12 [], and resulting alignments were post-processed using gblocks, version 0.91b [], using the following parameters: the minimum number of sequences for a conserved position […]


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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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