Proportal Strains

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(Another batch of genomes)
(Strain Discussion)
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=Strain Discussion=
=Strain Discussion=
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==Single cell genomes==
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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.
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Access this "single" database via biome.mit.edu through sql queries.
==More new genomes coming==
==More new genomes coming==

Revision as of 17:17, 30 January 2012

Contents

Strain Discussion

Single cell genomes

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/

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