Build custom database with accession

User Questions
1

Hello,

I´m trying to build a custom database with some missing sequences. In order to build a clean abin file i´m preparing a file with accession number as follows. The following sequences are not available at NCBI but they have a taxonomic id in the taxonomy database from ncbi.

My fasta file looks like this
>UQO_contig00001.1_1
VAVVVKVVLGRYVKNVGLKVNSDSLVNSGQEAKLDSIVSASTLVAA
AIFISFGLSLEAYLGAIISIIIIKSGIDMIRNTISQLLGERNDPELAREVRKTVEDFPGV
EGAYDLVLNNYGPDTWNGSIHIEVPDMIRNTISQLLGERNDPELAREVRKTVEDFPGV
EGAYDLVLNNYGPDTWNGSIHIEVPDTYTSDKLDQMIRDIQLEVYFKHQIILTAIGVYSI
NTQDPYVIAMHKKLKEIVFSHKYVTQLHGFYVDKSEKTIRFDVVISLDADDRLKIFEGVV
KDVESKFPEYEIEAFPDVDFTGV*
>UQO_contig00001.1_2
MRKLQDLKKQDENAAEREKQIVKTSVVGIIANVVLAAIKAIVGLASNSIAIILDAVNNIS
DAGSSLITIVGTKLAAKDPDKEHPFGYGRVEYLSAMIISVIVLYAGITSLVEAIKKIMNP
VIPTYTTPSLIIVAVAVVVKVVLGRYVKNVGLKVNSDSLVNSGQEAKLDSIVSASTLVAA
AIFISFGLSLEAYLGAIISIIIIKSGIDMIRNTISQLLGERNDPELAREVRKTVEDFPGV
EGAYDLVLNNYGPDTWNGSIHIEVPDTYTSDKLDQMIRDIQLEVYFKHQIILTAIGVYSI
NTQDPYVIAMHKKLKEIVFSHKYVTQLHGFYVDKSEKTIRFDVVISLDADDRLKIFEGVV
KDVESKFPEYEIEAFPDVDFTGV*

I have prepared the following file (accession and gi are the same in this case since those sequences are not referenced at ncbi). taxid is the correct one for that particular species.

accession accession.version taxid gi
UQO_contig00001.1_1 UQO_contig00001.1_1 1161098 UQO_contig00001.1_1
UQO_contig00001.1_2 UQO_contig00001.1_2 1161098 UQO_contig00001.1_2
UQO_contig00001.1_3 UQO_contig00001.1_3 1161098 UQO_contig00001.1_3
UQO_contig00001.1_4 UQO_contig00001.1_4 1161098 UQO_contig00001.1_4

Would that be the correct way(file format) for building the accession2taxid abin file ??

2

to add to an incomplete mapping, in addition to the abin file, you can also specify an “synonyms” file, and the lines should be formatted like this:
UQO_contig00001.1_1 tab taxon-id
UQO_contig00001.1_2 tab taxon-id
…
Then, specify both the .abin file (as accession mapping file) and your .map file containing such lines as a synonyms file and that should work.

3

Ok great Daniel ,
Thanks