Proportal Strains

Strain Discussion

Single cell genomes

January 30, 2012

The single cell genomes are already organized into an sql database on biome.mit.edu. Easy to extract proteins, contigs, all proteins that are Pro-core, or Pro&Syn-core, top hit in nr, etc.. Proteins are also assigned to ProPortal clusters.

Access this "single" database via biome.mit.edu through sql queries.

More new genomes coming

The 96 .gbk files on the Darwin cluster are at:/scratch/kashtan/Annotated/BATS_ALL/

Another batch of genomes

All of the new genomes are on Darwin, at /home/sbiller/newgenomes... in there are subdirectories for the FASTA files of contigs, the RAST annotation genbank files, and the amino acid sequences as determined by RAST.

New genomes to be added,

Strain Name	header 2	header 3
BATS_4A1C3_ace119	row 1, cell 2	row 1, cell 3
C12B_closedv3	row 1, cell 2	row 1, cell 3
GP2	row 1, cell 2	row 1, cell 3
LG	row 2, cell 2	row 2, cell 3
MIT0601_ace8	row 2, cell 2	row 2, cell 3
MIT0602_ace7	row 2, cell 2	row 2, cell 3
MIT0603_ace14	row 2, cell 2	row 2, cell 3
MIT9107	row 2, cell 2	row 2, cell 3
MIT9116	row 2, cell 2	row 2, cell 3
MIT9123	row 2, cell 2	row 2, cell 3
MIT9201	row 2, cell 2	row 2, cell 3
MIT9302	row 2, cell 2	row 2, cell 3
MIT9311	row 2, cell 2	row 2, cell 3
MIT9314	row 2, cell 2	row 2, cell 3
MIT9321	row 2, cell 2	row 2, cell 3
MIT9322	row 2, cell 2	row 2, cell 3
MIT9401	row 2, cell 2	row 2, cell 3
SA-C3	row 2, cell 2	row 2, cell 3
SA-E2	row 2, cell 2	row 2, cell 3
SA-E6	row 2, cell 2	row 2, cell 3
SB	row 2, cell 2	row 2, cell 3
SS2	row 2, cell 2	row 2, cell 3
SS35	row 2, cell 2	row 2, cell 3
SS51	row 2, cell 2	row 2, cell 3
SS52	row 2, cell 2	row 2, cell 3

MIT-9312

Case closed.

P-SSP6

Here is a feature that needed to be added to the genome of the phage P-SSP6.

    gene            complement(33508..33801)
                    /locus_tag="PRUG_00040a"
                    /note="Manually added and annotated 09-15-11 by SJL"
    CDS             complement(33508..33801)
                    /locus_tag="PRUG_00040a"
                    /codon_start=1
                    /transl_table=11
                    /product="High light inducible protein"
                    /protein_id="CAMERA-phage:PRUG_00040aT0"
                    /translation="EEVSRLAARTVHRHRHANLSFFQMVTTEYGKQNIFATEPQVQVL
                    TMDNENAEIQKWPLGYGRILGGHRCLCHHRTNHSWNLLNLIFFNDNSHTNKTK"
                    /note="Manually added and annotated 09-15-11 by SJL"

The GenBank file of P-SSP6 is attached.

P-SSS3

Here's the Broad FTP for P-SSS3, there's no Genbank file but there is some annotation:

ftp://ftp.broadinstitute.org/BIN/Annotation/broadAnnotation/20100304-dataRelease/P-SSS3/