computer_resources:assemblies:mitochondrion
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computer_resources:assemblies:mitochondrion [2011/07/10 22:39] karplus [Annotation] |
computer_resources:assemblies:mitochondrion [2015/07/16 18:33] ceisenhart Deleting this page |
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| - | ====== Mitochondrion ====== | ||
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| + | ===== Mitochondrial sequence ===== | ||
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| + | The mitochondrion was re assembled in 2015, follow the new assembly here, [[::mitochondrion_2015 | 2015 Mitochondrion assembly ]]. This page is for the 2012 mitochondrial assembly. | ||
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| + | The first draft sequence is available as {{mitochondrion-draft1.fasta.gz|draft1 gzipped fasta file}}. This corresponds to /campusdata/BME235/assemblies/slug/barcode-of-life/map-Illumina-raw-45/consensus-6 on campusrocks. It has 23,642 bases. | ||
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| + | ====== Mitochondrion ====== | ||
| The mitochondrion was assembled by Kevin Karplus in the assemblies/slug/barcode-of-life/ directory. The reason for the strange name for the directory was that at first the attempt was just to recover the COX1 gene that is used for the [[http://www.boldsystems.org/|BOLD (barcode of life database)]] project to characterize eukaryotes by their mitochondrial sequences. When it became clear that the whole mitochondrial genome was well covered in the Illumina data, the project switched to trying to reconstruct the full mitochondrial genome. | The mitochondrion was assembled by Kevin Karplus in the assemblies/slug/barcode-of-life/ directory. The reason for the strange name for the directory was that at first the attempt was just to recover the COX1 gene that is used for the [[http://www.boldsystems.org/|BOLD (barcode of life database)]] project to characterize eukaryotes by their mitochondrial sequences. When it became clear that the whole mitochondrial genome was well covered in the Illumina data, the project switched to trying to reconstruct the full mitochondrial genome. | ||
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| - | ===== Mitochondrial sequence ===== | ||
| - | The first draft sequence is available as {{mitochondrion-draft1.fasta.gz|gzipped fasta file}}. This corresponds to /campusdata/BME235/assemblies/slug/barcode-of-life/map-Illumina-raw-45/consensus-6 on campusrocks. | ||
| + | The second draft sequence (with the short repeats expanded and the repeats ordered as best I can from the short-insert reads) is available as {{mitochondrion-draft2.fasta.gz|draft2 gzipped fasta file}}. This corresponds to /campusdata/BME235/assemblies/slug/barcode-of-life/map-Illumina-raw-47/draft on campusrocks. It has 36363 bases. | ||
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| + | **I no longer believe that this sequence is correct. I'm now fairly sure that the region that I assembled as repeats should actually have been assembled as variants from a heterogeneous population of mitochondria. We'll need long reads or PCR products to tell for sure. ** | ||
| ===== Annotation ===== | ===== Annotation ===== | ||
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| I looked for tRNA genes with [[http://lowelab.ucsc.edu/tRNAscan-SE/|tRNAscan-SE]] run locally, and only found 7, but tRNAscan is known to have problems with mitochondial tRNAs. I'll work with Todd Lowe later this summer to try to improve the tRNAscan covariance models to handle them better. | I looked for tRNA genes with [[http://lowelab.ucsc.edu/tRNAscan-SE/|tRNAscan-SE]] run locally, and only found 7, but tRNAscan is known to have problems with mitochondial tRNAs. I'll work with Todd Lowe later this summer to try to improve the tRNAscan covariance models to handle them better. | ||
| - | The 7 easy-to-find tRNA genes are Asp-GTC, SeC-TCA, Val-TAC, Pro-TGG, Ala-TGC, Thr-TGT, Met-CAT. I have not checked yet whether these are consistent with the right genetic code. | ||
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| - | I can find the large an | + | The 7 easy-to-find tRNA genes are Asp-GTC, SeC-TCA, Val-TAC, Pro-TGG, Ala-TGC, Thr-TGT, Met-CAT. These are not correctly labeled for the mitochondrial genetic code: TCA is codon TGA which is Trp in code 5, though the others are ok. |
| + | I expect to find many copies of tRNA genes, as the repeat regions are in a tRNA-rich area of homologous mitochondria. | ||
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