MITOS: Improved de novo metazoan mitochondrial genome annotation
Citations
1,604 citations
888 citations
Cites methods from "MITOS: Improved de novo metazoan mi..."
...These range from specialized applications such as MITOS (11), that were designed for a subset of organellar genomes and whose output requires little to no quality control or manual curation, to GeSeq, a flexible tool that allows the annotation of essentially any organellar genome (15)....
[...]
590 citations
Cites background or methods from "MITOS: Improved de novo metazoan mi..."
...2012), the most comprehensive database for mitogenomes, is known to contain many incorrect mitogenomic annotations (Bernt et al. 2013), which can lead to inaccurate research results....
[...]
...MITOS (Bernt et al. 2013) is an automated pipeline for the de novo annotation of metazoan mitogenomes and comes closest to what MitoAnnotator achieves....
[...]
...In addition, RefSeq (Pruitt et al. 2012), the most comprehensive database for mitogenomes, is known to contain many incorrect mitogenomic annotations (Bernt et al. 2013), which can lead to inaccurate research results....
[...]
495 citations
465 citations
References
88,255 citations
"MITOS: Improved de novo metazoan mi..." refers methods in this paper
...Systematic semi-automatic error screening using a list of rules based on tRNAscan-SE (Lowe and Eddy, 1997), ARWEN (Laslett and Canback, 2008), and BLAST (Altschul et al., 1990) searches as well as expert knowledge is used for MitoZoa (Lupi et al., 2010), a recently released new data base....
[...]
...Furthermore all raw data of BLAST and Infernal, a graphical representation of the structure of the ncRNAs predicted by the covariance models, and a file containing the gene order are available (lacking the anticodon information for tRNA-encoding genes)....
[...]
...It uses a novel strategy based on aggregating BLAST searches with previously annotated protein sequences to identify protein coding genes (Section 2.1), thereby avoiding the need for a built-in data base of specifically curated protein models....
[...]
...BLAST is used by MOSAS to search for open reading frames and rRNAs based on a local data base of query sequences (currently from insects only)....
[...]
...Protein coding genes are annotated by means of a sophisticated aggregation procedure based on BLAST searches, which allows for the detection of frameshifts, duplication events, and split genes....
[...]
9,629 citations
"MITOS: Improved de novo metazoan mi..." refers methods in this paper
...Systematic semi-automatic error screening using a list of rules based on tRNAscan-SE (Lowe and Eddy, 1997), ARWEN (Laslett and Canback, 2008), and BLAST (Altschul et al., 1990) searches as well as expert knowledge is used for MitoZoa (Lupi et al., 2010), a recently released new data base....
[...]
4,229 citations
"MITOS: Improved de novo metazoan mi..." refers background in this paper
...The most comprehensive and up-to-date resource for mitochondrial genomes and their annotation is NCBI RefSeq (Pruitt et al., 2007)....
[...]
...About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs....
[...]
3,855 citations
"MITOS: Improved de novo metazoan mi..." refers methods in this paper
...We implemented specialised parser for mitogenome annotations based on biopython (Cock et al., 2009) for this task....
[...]
...In the following we provide a detailed description of the individual components of MITOS....
[...]
2,754 citations
"MITOS: Improved de novo metazoan mi..." refers methods in this paper
...DOGMA (Wyman et al., 2004) is a semi-automated pipeline of methods dealing with both mitochondrial and chloroplast genomes....
[...]
...Automatic annotation of organellar genomes with DOGMA....
[...]
...COVE (Eddy and Durbin, 1994) is employed by DOGMA to identify tRNAs candidates based on secondary structure....
[...]