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Updated PhyloToL Part 1: GF assignment (markdown)

Katzlab 2024-08-14 04:31:58 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -47,9 +47,11 @@ PhyloToL part 1 for genomes takes as input genomic CDS, such as are available to
with the first ten digits representing a unique sample identifier. Each sequence in the CDS fasta file should be formatted as downloaded from GenBank: with the first ten digits representing a unique sample identifier. Each sequence in the CDS fasta file should be formatted as downloaded from GenBank:
>\>lcl|NC_000001.11_cds_NP_001005484.2_1 [gene=OR4F5] [db_xref=CCDS:CCDS30547.1,Ensembl:ENSP00000493376.2,GeneID:79501] [protein=olfactory receptor 4F5] [protein_id=NP_001005484.2] [location=join(65565..65573,69037..70008)] [gbkey=CDS] >\>lcl|NC_000001.11_cds_NP_001005484.2_1 [gene=OR4F5] [db_xref=CCDS:CCDS30547.1,Ensembl:ENSP00000493376.2,GeneID:79501] [protein=olfactory receptor 4F5] [protein_id=NP_001005484.2] [location=join(65565..65573,69037..70008)] [gbkey=CDS]
ATGAAGAAGGTAACTGCAGAGGCTATTTCCTGGAATGAATCAACGAGTGAAACGAATAACTCTATGGTGACTGAATTCAT ATGAAGAAGGTAACTGCAGAGGCTATTTCCTGGAATGAATCAACGAGTGAAACGAATAA
TTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGT CTCTATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCT
TTGGAAACCTTCTTATTGTCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCAACCTC... TCCTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATT
GTCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCAA
CCTCTGA...
And all of the CDS fasta files should be in a folder alongside the [Scripts](https://github.com/Katzlab/PhyloToL-6/blob/main/PTL1/Genomes/Scripts) and [Databases](https://github.com/Katzlab/PhyloToL-6/blob/main/PTL1/Genomes/Databases) folders, as above. And all of the CDS fasta files should be in a folder alongside the [Scripts](https://github.com/Katzlab/PhyloToL-6/blob/main/PTL1/Genomes/Scripts) and [Databases](https://github.com/Katzlab/PhyloToL-6/blob/main/PTL1/Genomes/Databases) folders, as above.