Genbank-Protein-Processing

GenBankParser/ contains a tweaked part from Darrell Ricke's BioTools. Thanks Darrell! The tweaks make the parser extract only protein sequences, along with their annotations. It operates on Genbank flat files.

genbankToFasta.bash will call the GenBankParser in a loop for all the files in a directory.

PutHeaderAndSeqInDB.m ingests annotated protein fasta data into an Accumulo database. PutHeaderAndSeqInDB_AllFiles.m will ingests an entire directory.

NEW: Now in parallel using pMatlab.

Snippets

Snippet of gbbct1.seq

LOCUS       AB000111               14024 bp    DNA     linear   BCT 02-DEC-2006
DEFINITION  Synechococcus elongatus PCC 6301 genes for ribosomal proteins,
            complete cds.
ACCESSION   AB000111
VERSION     AB000111.1  GI:2446888
KEYWORDS    .
SOURCE      Synechococcus elongatus PCC 6301 (Synechococcus leopoliensis SAG
            1402-1)
  ORGANISM  Synechococcus elongatus PCC 6301
            Bacteria; Cyanobacteria; Oscillatoriophycideae; Chroococcales;
            Synechococcus.
REFERENCE   1
  AUTHORS   Sugita,M., Sugishita,H., Fujishiro,T., Tsuboi,M., Sugita,C.,
            Endo,T. and Sugiura,M.
  TITLE     Organization of a large gene cluster encoding ribosomal proteins in
            the cyanobacterium Synechococcus sp. strain PCC 6301: comparison of
            gene clusters among cyanobacteria, eubacteria and chloroplast
            genomes
  JOURNAL   Gene 195 (1), 73-79 (1997)
   PUBMED   9300823
REFERENCE   2  (bases 1 to 14024)
  AUTHORS   Sugita,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-DEC-1996) Mamoru Sugita, Nagoya University, Center
            for Gene Research; Furo-cho, Nagoya, Aichi 464-01, Japan
            (E-mail:[email protected], Tel:81-52-789-3087,
            Fax:81-52-789-3081)
FEATURES             Location/Qualifiers
     source          1..14024
                     /organism="Synechococcus elongatus PCC 6301"
                     /mol_type="genomic DNA"
                     /strain="PCC 6301"
                     /db_xref="taxon:269084"
                     /clone="lambda D5"
                     /clone_lib="lambda dash II library"
     CDS             89..406
                     /note="unnamed protein product"
                     /codon_start=1
                     /transl_table=11
                     /protein_id="BAA22448.1"
                     /db_xref="GI:2446889"
                     /translation="MLARISELTKIGTTIFIVAIDQVAEPNSWGSSQLVLLAKIAGAL
                     KAIPPNPVCTSRHRQAASVSPFRSAIVGTLLQLEAIKNLLTVSVDTIQQNGVLFIFVA
                     LLR"

...

Snippet of gbbct1._aas

>BAA22448.1 /organism="Synechococcus elongatus PCC 6301" /molecule="DNA" /date="02-DEC-2006" Exons[89-406] /codon_start=1 /db_xref="GI:2446889" /protein_id="BAA22448.1" /note="unnamed protein product" /taxon_id="269084"  /taxonomy="Bacteria; Cyanobacteria; Oscillatoriophycideae; Chroococcales; Synechococcus." /strain="PCC 6301" /def="Synechococcus elongatus PCC 6301 genes for ribosomal proteins, complete cds."
MLARISELTKIGTTIFIVAIDQVAEPNSWGSSQLVLLAKIAGALKAIPPNPVCTSRHRQA
ASVSPFRSAIVGTLLQLEAIKNLLTVSVDTIQQNGVLFIFVALLR

...

Accumulo DB Table Snippets

root@instance> tables
Tseq
TseqDegT
TseqFieldT
TseqInfo
TseqRaw
TseqRawNumBases
TseqT
root@instance> scan -t Tseq
BAA22448.1 :Exons|89-406 []    1
BAA22448.1 :codon_start|1 []    1
BAA22448.1 :date|2006-12-02 []    1
BAA22448.1 :db_xref|GI:2446889 []    1
BAA22448.1 :def|Synechococcus elongatus PCC 6301 genes for ribosomal proteins, complete cds. []    1
BAA22448.1 :molecule|DNA []    1
BAA22448.1 :note|unnamed protein product []    1
BAA22448.1 :organism|Synechococcus elongatus PCC 6301 []    1
BAA22448.1 :strain|PCC 6301 []    1
BAA22448.1 :taxon_id|269084 []    1
BAA22448.1 :taxonomy|Bacteria; Cyanobacteria; Oscillatoriophycideae; Chroococcales; Synechococcus. []    1
root@instance> scan -t TseqT
Exons|89-406 :BAA22448.1 []    1
codon_start|1 :BAA22448.1 []    1
date|2006-12-02 :BAA22448.1 []    1
db_xref|GI:2446889 :BAA22448.1 []    1
def|Synechococcus elongatus PCC 6301 genes for ribosomal proteins, complete cds. :BAA22448.1 []    1
molecule|DNA :BAA22448.1 []    1
note|unnamed protein product :BAA22448.1 []    1
organism|Synechococcus elongatus PCC 6301 :BAA22448.1 []    1
strain|PCC 6301 :BAA22448.1 []    1
taxon_id|269084 :BAA22448.1 []    1
taxonomy|Bacteria; Cyanobacteria; Oscillatoriophycideae; Chroococcales; Synechococcus. :BAA22448.1 []    1
root@instance> scan -t TseqDegT
Exons|89-406 :deg []    1
codon_start|1 :deg []    1
date|2006-12-02 :deg []    1
db_xref|GI:2446889 :deg []    1
def|Synechococcus elongatus PCC 6301 genes for ribosomal proteins, complete cds. :deg []    1
molecule|DNA :deg []    1
note|unnamed protein product :deg []    1
organism|Synechococcus elongatus PCC 6301 :deg []    1
strain|PCC 6301 :deg []    1
taxon_id|269084 :deg []    1
taxonomy|Bacteria; Cyanobacteria; Oscillatoriophycideae; Chroococcales; Synechococcus. :deg []    1
root@instance> scan -t TseqFieldT
Exons :deg [] 5
codon_start :deg []    5
date :deg []    5
db_xref :deg []    5
def :deg []    5
ec_number :deg []    1
gene :deg []    3
molecule :deg []    5
note :deg []    2
organism :deg []    5
product :deg []    3
strain :deg []    5
taxon_id :deg []    5
taxonomy :deg []    5
root@instance> scan -t TseqRaw
BAA22448.1 :seq []    MLARISELTKIGTTIFIVAIDQVAEPNSWGSSQLVLLAKIAGALKAIPPNPVCTSRHRQAASVSPFRSAIVGTLLQLEAIKNLLTVSVDTIQQNGVLFIFVALLR
root@instance> scan -t TseqRawNumBases
BAA22448.1 :num []    105
root@instance> scan -t TseqInfo
gbbct1._aas :statNumBasePut []    1.53868e+07
gbbct1._aas :statNumMetaPut []    663812
gbbct1._aas :statNumSeqPut []    53229
gbbct1._aas :statTimePut []    655.389