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Protocols

RASCAL specifications

Information


Unique identifier OMICS_33203
Name RASCAL
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some multiple alignments.
Input format MSF,FASTA
Output data The new refined alignment.
Output format MSF,FASTA
Operating system Unix/Linux
Programming languages Other
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Olivier Poch

Publication for RASCAL

RASCAL citations

 (103)
library_books

HMMER Cut off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut off threshold

2018
PLoS One
PMCID: 5868777
PMID: 29579071
DOI: 10.1371/journal.pone.0193757

[…] ccepted. MSAs were constructed by MAFFTv7 [] using the slow iterative global refinement (FFT-NS-i) mode for PGs and the multiple domain iteration (E-INS-i) mode for PLCs and subsequently corrected by Rascal []. PHYML3 [] using the LG model was used for phylogenetic tree reconstruction following BMGE [] trimming with BLOSUM62 matrix and an entropy cut-off of 0.9. Complete trees were constructed wit […]

library_books

Drugs and Mental Health Problems among the Roma: Protective Factors Promoted by the Iglesia Evangélica Filadelfia

2018
PMCID: 5858404
PMID: 29443877
DOI: 10.3390/ijerph15020335

[…] rothers died because of drugs. However, he notes that his active participation in the church since he was 15 acted as the impetus that allowed him to get away from drugs:“At 15 years old, I was not a rascal but I was a sort of a dissolute lad, and I was aware that this would not end well (...) A Roma pastor entered the church and simply bet on me. To be baptized in the Iglesia Evangélica Filadelfi […]

library_books

Growing old, yet staying young: The role of telomeres in bats’ exceptional longevity

2018
Sci Adv
PMCID: 5810611
PMID: 29441358
DOI: 10.1126/sciadv.aao0926

[…] ation workflow, which compares MUSCLE (multiple sequence comparisonb y log-expectation) () and MAFFT (multiple alignment using fast fourier transform) (, ) alignments, applies a refinement step using RASCAL (), and provides a norMD () score as a measure of alignment quality. Alignments were further optimized using the phylogeny-aware aligner Prank () by aligning as codons, using six iterations of […]

library_books

First bone cracking dog coprolites provide new insight into bone consumption in Borophagus and their unique ecological niche

2018
eLife
PMCID: 5963924
PMID: 29785931
DOI: 10.7554/eLife.34773.023

[…] , it signaled the potential for discovery of vertebrate fossils in the Mehrten Formation, as well as associated plants (; ). A partial skull of Megalonyx mathisi was described subsequently from Black Rascal Creek in ‘Upper Mehrten Formation’ (). Systematic collecting of fossils in the Turlock Lake area, mostly by one of us (DG), was carried out in as early as the 1950 s. In an unpublished Ph.D. di […]

library_books

Analysis of viral diversity for vaccine target discovery

2017
BMC Med Genomics
PMCID: 5763473
PMID: 29322922
DOI: 10.1186/s12920-017-0301-2

[…] le regions (about 200–500 sequences per region). These smaller region subsets are then aligned using MUSCLE, PROMALS3D [] or CLUSTAL W/X [] for the most reliable alignment, which is then refined with RASCAL [] before merging the subsets into a full protein multiple sequence alignment by use of conserved domain/motifs as anchors. The final protein alignments are manually inspected and corrected for […]

library_books

Mutational analysis of KRAS and its clinical implications in cervical cancer patients

2017
PMCID: 5709530
PMID: 29185262
DOI: 10.3802/jgo.2018.29.e4

[…] ognostic marker in non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) []. In a large cohort of patients with CRC, the multicenter Refractory Angina Spinal Cord stimulation and usuAL care (RASCAL) study demonstrated that the KRAS G12V mutation exerted more aggressive properties than other KRAS mutations regarding disease recurrence and death []. In BRAF wild-type CRC, Imamura reported t […]

Citations

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RASCAL institution(s)
Laboratoire de Biologie et Genomique Structurales, Institut de Genetique et de Biologie Moleculaire et Cellulaire (CNRS/INSERM/ULP), Illkirch, France
RASCAL funding source(s)
Supported by institute funds from the Institut National de la Sante et de la Recherche Medicale, the Centre National de la Recherche Scientifique, the Hopital Universitaire de Strasbourg, the Fond National de la Science (GENOPOLE) and the Fond de Recherche Hoechst Marion Roussel.

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