Difference between revisions of "Genome comparisons"
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We would like to edit the Perl tool that currently compares start and stop codons from the same species in three different annotations, or find an existing tool that will do the following: We would like this tool to compare our Halomicrobium mukohataei genome to 9 other halophile’s genomes all using the annotations from RAST. Basically, the Perl script should take all the known H. mukohataei amino acid sequences from RAST and compare these (in a Blastp manner) to all 9 other halophile genomes. In this manner, we will be able to determine which genes in H. mukohataei are conserved among other halophiles and which are unique to this species. The other 9 species we would like to compare are: <br> | We would like to edit the Perl tool that currently compares start and stop codons from the same species in three different annotations, or find an existing tool that will do the following: We would like this tool to compare our Halomicrobium mukohataei genome to 9 other halophile’s genomes all using the annotations from RAST. Basically, the Perl script should take all the known H. mukohataei amino acid sequences from RAST and compare these (in a Blastp manner) to all 9 other halophile genomes. In this manner, we will be able to determine which genes in H. mukohataei are conserved among other halophiles and which are unique to this species. The other 9 species we would like to compare are: <br> | ||
[[Haloarcula sp 33799]] (Karen) <br> | [[Haloarcula sp 33799]] (Karen) <br> | ||
| − | [[Haloarcula | + | [[Haloarcula sinaiiensis 33800]] (Claudia) <br> |
[[Haloarcula vallismortis]] (Katie) <br> | [[Haloarcula vallismortis]] (Katie) <br> | ||
| − | [[Haloferax denitrificans]] ( | + | [[Haloferax denitrificans]] (Megan)<br> |
| − | [[Haloferax mediterranei]] <br> | + | [[Haloarcula californiae]] (Megan)<br> |
| − | [[Haloferax mucosum]] <br> | + | [[Haloferax mediterranei]] (Claudia)<br> |
| + | [[Haloferax mucosum]] (Sarah) <br> | ||
[[Haloferax sulfurifontis]] (Sarah) <br> | [[Haloferax sulfurifontis]] (Sarah) <br> | ||
[[Haloferax volcanii]] (Sarah) <br> | [[Haloferax volcanii]] (Sarah) <br> | ||
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The complete amino acid sequences for each of these species will be needed to do this comparison. A link to each of these sequences can be found below: | The complete amino acid sequences for each of these species will be needed to do this comparison. A link to each of these sequences can be found below: | ||
| − | [ | + | [http://www.bio.davidson.edu/courses/Bio343/2009/carcelen/Haloarcula_sinaiiensis_ATCC_33800.fasta ''Haloarcula sinaiiensis'' ATCC 33800 FASTA Format]<br> |
| − | + | [http://www.bio.davidson.edu/courses/Bio343/2009/Reilly/Haloarcula_vallismortis_ATCC_29715.fasta ''Haloarcula vallismortis'' ATCC 29715 FASTA Format]<br> | |
| − | [ | + | [http://www.bio.davidson.edu/courses/Bio343/2009/hasty/Haloarcula_californiae_ATCC_33799.fasta ''Haloarcula californiae'' ATCC 33799 FASTA Format]<br> |
| − | [ | + | [http://www.bio.davidson.edu/courses/Bio343/2009/Reilly/Haloferax_denitrificans_ATCC_35960.fasta ''Haloferax denitrificans'' ATCC 35960 FASTA Format]<br> |
| − | [ | + | [http://www.bio.davidson.edu/courses/Bio343/2009/hasty/Haloferax_mediteranei_ATCC_33500.fasta ''Haloferax mediteranei'' ATCC 33500 FASTA Format]<br> |
| − | [ | + | [http://www.bio.davidson.edu/courses/Bio343/2009/richeson/Haloferax_volcanii_ATCC_29605.fasta ''Haloferax volcanii'' ATCC 29605 FASTA Format]<br> |
| − | [ | + | [http://www.bio.davidson.edu/courses/Bio343/2009/carcelen/Haloferax_sulfurifontis_ATCC_BAA-897.fasta ''Haloferax sulfurifontis'' ATCC BAA-897 FASTA Format]<br> |
| − | [ | + | [http://www.bio.davidson.edu/courses/Bio343/2009/pyfrom/Haloferax_mucosum_ATCC_BAA-1512.fasta Haloferax ''mucosum'' ATCC BAA 1512 FASTA Format]<br> |
| − | [ | + | [http://www.bio.davidson.edu/courses/Bio343/2009/Hasty/Halomicrobium_mukohataei_DSM_12286.fasta ''Halomicrobium mukohataei'' DSM 12286 FASTA Format]<br> |
| − | [ | ||
Latest revision as of 16:32, 29 October 2009
We would like to edit the Perl tool that currently compares start and stop codons from the same species in three different annotations, or find an existing tool that will do the following: We would like this tool to compare our Halomicrobium mukohataei genome to 9 other halophile’s genomes all using the annotations from RAST. Basically, the Perl script should take all the known H. mukohataei amino acid sequences from RAST and compare these (in a Blastp manner) to all 9 other halophile genomes. In this manner, we will be able to determine which genes in H. mukohataei are conserved among other halophiles and which are unique to this species. The other 9 species we would like to compare are:
Haloarcula sp 33799 (Karen)
Haloarcula sinaiiensis 33800 (Claudia)
Haloarcula vallismortis (Katie)
Haloferax denitrificans (Megan)
Haloarcula californiae (Megan)
Haloferax mediterranei (Claudia)
Haloferax mucosum (Sarah)
Haloferax sulfurifontis (Sarah)
Haloferax volcanii (Sarah)
Halorhabdus utahensis (Karen)
The complete amino acid sequences for each of these species will be needed to do this comparison. A link to each of these sequences can be found below:
Haloarcula sinaiiensis ATCC 33800 FASTA Format
Haloarcula vallismortis ATCC 29715 FASTA Format
Haloarcula californiae ATCC 33799 FASTA Format
Haloferax denitrificans ATCC 35960 FASTA Format
Haloferax mediteranei ATCC 33500 FASTA Format
Haloferax volcanii ATCC 29605 FASTA Format
Haloferax sulfurifontis ATCC BAA-897 FASTA Format
Haloferax mucosum ATCC BAA 1512 FASTA Format
Halomicrobium mukohataei DSM 12286 FASTA Format
