The taxdump files from NCBI, along with the 'nr' database, are often used in meta -genomics and -transcriptomics software to inform taxonomic identification of reads, contigs and ORFs. However, if you are working with organisms that have little to no representation in the NCBI databases then you may find yourself a bit stuck.
Many researchers in this situation will have custom databases of genomic/transcriptomic data and want to use it, but may still find their organism(s) unavailable within the NCBI taxonomy DB. If your organism does not have a valid TaxID in NCBI then you are unable to use many of the software packages that rely on 'taxdump' to extract taxonomic lineage and naming information with your custom DBs.
This tool will allow you to modify the 'taxdump' (appending new data to names.dmp and nodes.dmp) files from NCBI, to temporarily include your organisms - until they find represenration of their own in the NCBI taxonomy lineage.
The script will automatically find the largest taxonomic ID in nodes.dmp and increment from that point (with a 10^length-1 addition) and assign it to your new taxa. This large addition is to avoid future conflicts with taxdump updates. Once added, you can then run makeblastdb with the '-taxid' option and your newly assigned TaxID.
taxdump_edit.pl -names names.dmp -nodes nodes.dmp -taxa NAME -parent XXX -rank NAME -division X
Required Input:
-names names.dmp location
-nodes nodes.dmp location
-taxa new taxa/group name
-parent parent TaxID
-rank rank name (see -help)
-division division ID (see -help)
Optional Input
-override TaxID from previous
Optional Input (names.dmp):
unique name
Default Values (names.dmp):
name class (scientific name) (see -help)
Optional Input (nodes.dmp):
embl code
genetic code (1) (see -help)
mitochondria genetic code (1) (see -help)
comments
Default Values (nodes.dmp):
inherited div flag = 1
inherited GC flag = 1
inherited MGC flag = 1
GenBank hidden flag = 1
hidden subtree root flag = 1
Adding a new 'species' lineage, for example, MAST-4A. We know by looking at the NCBI Taxonomy that there is already a group for "Stramenopiles MAST-4" at TaxID:1735725 with a lineage of "cellular organisms; Eukaryota; Stramenopiles; unclassified stramenopiles". This is correct for our new organism, so we need to note down the TaxID of '1735725'. Then use the script as below, this assumes some default options which have been noted in the Usage section above:
taxdump_edit.pl -names names.dmp -nodes nodes.dmp -taxa MAST-4A -parent 1735725 -rank species -division 11
We have given the script the location of both names.dmp and nodes.dmp, along with the new taxa name of 'MAST-4A'. We are saying that the parental lineage is TaxID:1735725 and that the rank of the organism is 'species'. The division number is from the Division list below, and is 'Environmental Samples' - number 11 - to reflect the provenance of our sample and unlike many other Stramenopiles in NCBI which are listed as '4' - Plants and Fungi. :/
This will show the output:
Your calculated TaxID = 3304349. Please use this with makeblastdb and your fasta sequences.
Backing up orginal names.dmp
Appending new line
Done.
Backing up orginal nodes.dmp
Appending new line
Finished.
Remember your new TaxID of '3304349', this is the ID you will need to use with makeblastdb.
At the end of the names.dmp file, you will now have a new record:
3304349 | MAST-4A | | scientific name |
Along with the corresponding record in nodes.dmp
3304349 | 1735725 | species | | 11 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
The original nodes.dmp and names.dmp have been backed up in the same location as nodes_backup.dmp and names_backup.dmp.
This is done much in the same way, but you will have to add the different lineage levels one-by-one in order to build the taxonomic relationships. However, we don't want the TaxID to keep on incrementing by 10^length-1, so we can use the -override variable to supply the script with the previous TaxID and it will increment it by 1. Add the 'lowest' rank of your new lineage first, e.g. kingdom before class and then finally genus and species.
0 -> Bacteria
1 -> Invertebrates
2 -> Mammals
3 -> Phages
4 -> Plants and Fungi
5 -> Primates
6 -> Rodents
7 -> Synthetic and Chimeric
~~8 -> Unassigned - Do Not Use~~
9 -> Viruses
10 -> Vertebrates
11 -> Environmental Samples
0 -> Unspecified
1 -> Standard
2 -> Vertebrate Mitochondrial
3 -> Yeast Mitochondrial
4 -> Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
5 -> Invertebrate Mitochondrial
6 -> Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
9 -> Echinoderm Mitochondrial; Flatworm Mitochondrial
10 -> Euplotid Nuclear
11 -> Bacterial, Archaeal and Plant Plastid
12 -> Alternative Yeast Nuclear
13 -> Ascidian Mitochondrial
14 -> Alternative Flatworm Mitochondrial
15 -> Blepharisma Macronuclear
16 -> Chlorophycean Mitochondrial
21 -> Trematode Mitochondrial
22 -> Scenedesmus obliquus mitochondrial
23 -> Thraustochytrium mitochondrial code
24 -> Pterobranchia Mitochondrial
25 -> Candidate Division SR 1 and Gracilibacteria
26 -> Pachysolen tannophilus Nuclear
27 -> Karyorelict Nuclear
28 -> Condylostoma Nuclear
29 -> Mesodinium Nuclear
30 -> Peritrich Nuclear
31 -> Blastocrithidia Nuclear
Acronym
Anamorph
Authority
Blast Name
Common Name
Equivalent Name
Genbank Acronym
Genbank Anamorph
Genbank Common Name
Genbank Synonym
Includes
In-part
Misnomer
Misspelling
Scientific Name
Synonym
Teleomorph
Type Material
no rank
superkingdom
kingdom
subkingdom
superphylum
phylum
subphylum
superclass
class
subclass
infraclass
cohort
superorder
order
suborder
infraorder
parvorder
superfamily
family
subfamily
tribe
subtribe
genus
subgenus
species group
species
species subgroup
subspecies
varietas
forma
As per NCBI's taxdump_readme.txt: Each of the files store one record in the single line that are delimited by "\t|\n" (tab, vertical bar, and newline) characters. Each record consists of one or more fields delimited by "\t|\t" (tab, vertical bar, and tab) characters. The brief description of field position and meaning for each file follows.
This file represents taxonomy nodes. The description for each node includes the following fields:
tax_id -- node id in GenBank taxonomy database
parent tax_id -- parent node id in GenBank taxonomy database
rank -- rank of this node (superkingdom, kingdom, ...)
embl code -- locus-name prefix; not unique
division id -- see division.dmp file
inherited div flag (1 or 0) -- 1 if node inherits division from parent
genetic code id -- see gencode.dmp file
inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent
mitochondrial genetic code id -- see gencode.dmp file
inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent
GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage
hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet
comments -- free-text comments and citations
Taxonomy names file has these fields:
tax_id -- the id of node associated with this name
name_txt -- name itself
unique name -- the unique variant of this name if name not unique
name class -- (synonym, common name, ...)
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
tar zxvf taxdump.tar/gz
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_readme.txt
