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cDNA2Genome specifications

Information


Unique identifier OMICS_24911
Name cDNA2Genome
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A cDNA sequence.
Output data A summary including sequence identifier, description, and scores of the most important hits found for each of the homology searches performed, a graphical output placing the cDNA at its corresponding position in a human chromosome and graphical output shows open reading frames (ORFs) in each of the three forward frames.
Output format XML+HTML
Computer skills Basic
Stability No
Maintained No

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Publication for cDNA2Genome

cDNA2Genome citations

 (6)
library_books

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis Associated Genes

2018
Genes
PMCID: 5924527
PMID: 29597328
DOI: 10.3390/genes9040185

[…] y 3 bp for the top hits and by 9 bp for the secondary hits. Transcripts of B. stricta (assembly v1.2, []) with marked CDS regions were also aligned to the B. retrofracta genome by Exonerate using the cDNA2Genome model leaving the other options unchanged. Alignments of CDS segments were not cut for top hits, but cut by 3 bp for secondary hits. These truncated fragments were clustered and supplied a […]

library_books

Regulatory remodeling in the allo tetraploid frog Xenopus laevis

2017
Genome Biol
PMCID: 5655803
PMID: 29065907
DOI: 10.1186/s13059-017-1335-7

[…] Orthologs of X. tropicalis were searched in the genome of X. laevis with the cdna2genome tool from Exonerate []. From 14,500 sequences submitted, 14,276 were successfully scanned. From those, 10,935 found a match in both subgenomes, leaving 3343 sequences that did not return a […]

library_books

The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies

2017
BMC Genomics
PMCID: 5603072
PMID: 28915793
DOI: 10.1186/s12864-017-4120-9

[…] .Then, as discrepancies are possible, we performed some quality checks by comparing protein-coding sequences before and after the transfer. For the remaining non-transferred genes, we used Exonerate (cdna2genome model), with the same selection criteria.Furthermore, a new de novo RefSeq structural annotation, was performed by the NCBI Eukaryotic Genome Annotation Pipeline with the methodology descr […]

library_books

The Ensembl gene annotation system

2016
PMCID: 4919035
PMID: 27337980
DOI: 10.1093/database/baw093

[…] Protein-coding models generated from protein-to-genome alignments in the Targeted, Similarity and Ortholog recovery pipelines will not have UTRs annotated. Targeted models produced by Exonerate’s cdna2genome model, on the other hand, do not require UTR extension because they are based on the alignment of cDNA and will already have UTRs annotated.Models made from RNA-seq, cDNA or EST sequences […]

library_books

Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi automated bioinformatics methods

2016
BMC Genomics
PMCID: 4793746
PMID: 26984673
DOI: 10.1186/s12864-016-2579-4

[…] tations from the first draft genome sequence to the new assembly. Gene annotations (consisting in fasta putative transcripts) were transferred to the new assembly using Exonerate software [] with the cdna2genome model and a maximum allowed intron size of 30 kb. Exonerate performed genomic searches and spliced alignments in a single run. Using a custom Perl script, based on the exonerate output, we […]

library_books

The non obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes

2013
PMCID: 3668384
PMID: 23729657
DOI: 10.1093/database/bat032

[…] 57BL/6J and NOD. Genes are categorized not only at the gene level but also at the transcript level, definitions of which can be found in Vega (). Gene structures were transferred using exonerate’s () cdna2genome model to align transcripts between the C57BL/6J and NOD mouse strains where clear homology existed and verified. Where clear homologs could not be identified, the gene models were built in […]

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cDNA2Genome institution(s)
Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Heidelberg, Germany

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