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

[Zhiqiang Ye]

you can just run dbifasta, you don't need formatdb.

　　

======= 2003-04-22 13:57:00 您在来信中写道：=======

>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
>-----------------------------------------------------------------

= = = = = = = = = = = = = = = = = = = =
			

Best Wishes!                    
				 
               Zhiqiang Ye
					2003-04-23