To specifically answer the question the search that is used is
((1000:1500[Sequence Length]) AND Piscirickettsia salmonis[Organism]) AND 16S
That is place here and select 'nucleotide'.
Genbank uses taxon id internally, it's a database reference not a biological code, and can't be used as input - its completely unique to Genbank. Anyway the search results in 276 records, and are shown here, this is near full length 16S thats cool.
[taxon id] is not a field in Genbank, it's a database code, the tag is
[organism]. Genbank knows what 16S is - its the most famous genetic marker in microbiology - so there is no need for a
At the base of the page there is a "Send to:" option (right hand corner). Click and then select "File". The 276 sequences will then download.
[Sequence length] is removed this result 3820 sequences here. There are some 16S-23S sequences on the database result in a 2,198 bp length, so extending the sequence length will trap these by
1000:2200[Sequence Length]. There are 431 bp sequences - which are not cool at all, probably a lot.
The approach used below identifies nearly 1000 is complicated it traps everything of relevance which is close to full length and cuts out the 16S from 2,198 bp length and beyond. The 431 bp partial 16S sequences have been removed. Thus the numbers below are the idealised data set, so its about 1000 sequences and the tree will guide you into major groups - which is probably what is wanted, i.e. to place a 16S from a local salmon farm into the broader clade diversity of the species.
The answer is for this species is there are around a thousand sequences on Genbank for the species of interest which are split into 6 identical genotypic groups. The demonstration of the species is represented by the scale bar, i.e. it is very little genetic diversity.
Cycloclausticus sp is the outgroup and each member of the in-group is Piscirickettsia salmonis
Just to address the comments
- "Cycloclasticus"? The question is not specific to /db_xref="taxon:1238"
It is specific there's a fundamental principle of trees. A tree needs a root, all the ingroups are all Piscirickettsia salmonis. Without a root, i.e. something that is not Piscirickettsia salmonis there is no direction in the tree. Cycloclasticus is a good or reasonable root.
- how do i access this interface?
Its complicated to explain and its a different question.