computer_resources:assemblies:mitochondrion
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computer_resources:assemblies:mitochondrion [2014/10/23 03:15] karplus [Mitochondrial sequence] |
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|draft1 gzipped fasta file}}. This corresponds to /campusdata/BME235/assemblies/slug/barcode-of-life/map-Illumina-raw-45/consensus-6 on campusrocks. It has 23642 bases. | ||
| 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. | 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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