database ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/April_14_2003/ for emboss

[Zheng Jin Tu]

Here is some more message related to this question:

on .embossrc file:

  DB chr16 [
        type:           N
        method:         blast
        release:        "33"
        format:         ncbi
        dir:            /usr/local/db/embossdb/H_sapiens/build_33/CHR_16up
        file:           chr16.fa*
        comment:        "Human chr 16 from ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/April_14_2003/"
  ]



Then try to run

fuzztran -sequence=chr16 -pattern="CC" -mismatch=0 -frame=6 -outf=myout
Protein pattern search after translation

   EMBOSS An error in ajseqdb.c at line 4006:
error reading file
/usr/local/db/embossdb/H_sapiens/build_33/CHR_16up/chr16.fa.nhr



Thanks,


Tu


----------------------------------------------------------------
Zheng Jin Tu
Computational Biology Specialist
Supercomputing Institute
599 Walter Library
117 Pleasant Street SE
University of Minnesota
Minneapolis, Minnesota 55455
email: ztu at msi.umn.edu            help email:  help at msi.umn.edu
phone: 612-624-9504, 624-0115     help phone:  612-626-0802
fax:   612-624-8861
-----------------------------------------------------------------

On Tue, 22 Apr 2003, Zheng Jin Tu wrote:

>
> Anyone has success story in "indexing" human genome at
> ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/April_14_2003/
> for emboss?
>
> They are fasta format files, I try to run formatdb these chromosomes
> then dbiblast.  But it always gives me some errors.
>
>
> Some runs as
>
> ----------------------------------------------
> swinst at bi7 [CHR_16up] % head chr16.fa
> >gi|29824587|ref|NC_000016.4|NC_000016 Homo sapiens chromosome 16,
> complete sequence
> TAACCCTAACCCTAACCCTAACCCTAACCCTAACCGACCCTCACCCTCACCCTAACCACATGAGCAATGT
> GGGTGTTATATTTTAGCTGTCATGGGTGCATTAGGAATGCTGCATTTGTGTTTCAACGCTGCAACTGGAC
> CCTGCAATGCAGCCCCTCGCCTTGCCTTGGGAGAATCTCGGTGCCCAGGATTCAGAGGGGCTTTTAGTTT
> CCCATTTTCCACACTGAACCGTTCTAACTGGTCTCTGACCTTGATTATTCACGGCTGCAACCGGGAAAGA
> TTTTATTCACTGTCAATGCGCCCCGAGTTGTCCCAAAGCCAGGCAGTGCCCCCAACGTCTGTGCTTAGCA
> GAATGCTGCTCCACCTTTACGGTGACCCCCAGGTCTGTGCTGAGCAGAACGCAGCTCCGCCCTCGCAGTA
> CCCTCAGCCCGCCCGCCCGGGTCTGACCTGAGCAGAACTCTGCTCTGCCTTCGCAGTACCACCGAAATCT
> GTGCAAAGGAGAACGCAGCTCCGCCCTCGCGGTGCTCTCCGCGTCTGTGCTGAGGAGAACGCAACTCCGC
> CGTCGCAAAGGCGCGCGCCGCGCCGGCGCAGGCGCAGAGGGGCGCGCCGCGCCGGCGCAGGCGCAGAGAC
>
> swinst at bi7 [CHR_16up] % formatdb -i chr16.fa -p F -o T
> swinst at bi7 [CHR_16up] % ls -l chr16*
> -rw-r--r--    1 swinst   swinst     91281742 Apr 14 05:27 chr16.fa
> -rw-r-----    1 swinst   swinst          129 Apr 22 13:53 chr16.fa.nhr
> -rw-r-----    1 swinst   swinst           80 Apr 22 13:53 chr16.fa.nin
> -rw-r-----    1 swinst   swinst            8 Apr 22 13:53 chr16.fa.nnd
> -rw-r-----    1 swinst   swinst           52 Apr 22 13:53 chr16.fa.nni
> -rw-r-----    1 swinst   swinst          147 Apr 22 13:53 chr16.fa.nsd
> -rw-r-----    1 swinst   swinst           66 Apr 22 13:53 chr16.fa.nsi
> -rw-r-----    1 swinst   swinst     22518829 Apr 22 13:53 chr16.fa.nsq
>
> swinst at bi7 [CHR_16up] % dbiblast
> Index a BLAST database
> Database name: chr16
> Database directory [.]:
> Wildcard database filename [chr16]: chr16.fa*
> Release number [0.0]: 33
> Index date [00/00/00]: 04/22/03
>          N : nucleic
>          P : protein
>          ? : unknown
> Sequence type [unknown]: N
>          1 : wublast and setdb/pressdb
>          2 : formatdb
>          0 : unknown
> Blast index version [unknown]: 2
> swinst at bi7 [CHR_16up] % ls -rlt
> -rw-r-----    1 swinst   swinst            8 Apr 22 13:53 chr16.fa.nnd
> -rw-r-----    1 swinst   swinst           52 Apr 22 13:53 chr16.fa.nni
> -rw-r-----    1 swinst   swinst          147 Apr 22 13:53 chr16.fa.nsd
> -rw-r-----    1 swinst   swinst           66 Apr 22 13:53 chr16.fa.nsi
> -rw-r-----    1 swinst   swinst          129 Apr 22 13:53 chr16.fa.nhr
> -rw-r-----    1 swinst   swinst           80 Apr 22 13:53 chr16.fa.nin
> -rw-r-----    1 swinst   swinst     22518829 Apr 22 13:53 chr16.fa.nsq
> -rw-r--r--    1 swinst   swinst          680 Apr 22 13:53 formatdb.log
> -rw-r--r--    1 swinst   swinst          344 Apr 22 13:55 division.lkp
> -rw-r--r--    1 swinst   swinst          320 Apr 22 13:55 entrynam.idx
> -rw-r--r--    1 swinst   swinst          300 Apr 22 13:55 acnum.trg
> -rw-r--r--    1 swinst   swinst          300 Apr 22 13:55 acnum.hit
> swinst at bi7 [CHR_16up] %
>
> --------------------------------------------------------------------------
>
> Thanks,
>
>
> Tu
>
> ----------------------------------------------------------------
> Zheng Jin Tu
> Computational Biology Specialist
> Supercomputing Institute
> 599 Walter Library
> 117 Pleasant Street SE
> University of Minnesota
> Minneapolis, Minnesota 55455
> email: ztu at msi.umn.edu            help email:  help at msi.umn.edu
> phone: 612-624-9504, 624-0115     help phone:  612-626-0802
> fax:   612-624-8861
> -----------------------------------------------------------------
>
>