Welcome, everyone.
This is going to be a relatively short webinar today.
The introductory slide there gives you standard information.
Maybe one of the most important things is, feel free to ask questions in the question
pod during the webinar as you think of those questions.
We always have the questions and answers in a Materials link on the courses and webinars
page in archived webinars.
Just search NCBI courses and webinars and you will find the page.
Within a few days, this webinar, which is being recorded, will be on our YouTube channel
along with the others.
Please feel free to email me directly if you have questions afterward at matten@ncbi.nlm.nih.gov.
You can also send general BLAST questions to blast-help@ncbi.nlm.nih.gov . Sitting here
with me today is Christiam Camacho and Tom Madden, developers from the BLAST group.
You will get some very expert answers to your questions.
Peter Cooper is on the question pod answering questions during the webinar.
Let me go ahead and give you the take home message for today.
The take home message is we highly encourage you to upgrade to version 2.5.0 before November
9.
The next slide will tell you what will happen on November 9.
The first of the topics today has to do with a NCBI-wide switch to HTTPS from standard
HTTP, but this will particularly affect standalone BLAST in a couple of ways that I'll show you
on the next slide.
This change will take effect for APIs that deal with blast.
The general webpages have already made the change.
We will also talk about another change which is the phasing out of G.I.
numbers and how using the accession.version will impact standalone blast.
We will very briefly talk touch on a couple of improvements that came out in this release.
So, what's going to break on Nov 9 if you are still using version 2.4 .0 or earlier?
Primarily the remote option will not work.
If you send searches to our servers, that will fail to work unless you have upgraded
to 2.5.0 . Another function, some of you may or may not be using, but it is very handy,
and that is a prefetch function.
In the past, you could only use that with the remote option, but in this version, it
has been improved.
You can use it without the remote option.
What happens is you input a query file which contains identifiers, either GIs or accessions,
and the programs will fetch those IDs from NCBI.
You will not be able to use these two functions if you have not upgraded before November 9.
Having said that, we plan to have a test this coming Thursday, October 13 from 10 AM until
11 AM Eastern time.
In other words, try running version 2.4.0 and it should not work during that time but
2.5.0 should.
We may very well have other tests before the ninth.
We probably will.
Look on our webpages for an announcement for those tests.
Hopefully we will get an announcement out in the blast-announce email list for those
other upcoming tests.
The second major change has to do with phasing out GIs.
I have a couple of links in the last slides where you can get more general information
about both the HTTPS change and the phase out of gi's.
In terms of standalone BLAST , what will happen is you will be seeing more and more the new
style of definition lines versus the old-style.
In the old-style, the definition lines start with gi and then the pipe symbol and then
the number and so on.
We are moving now to just what we call bare accession.version.
Those of you who are downloading our FASTA databases from the BLAST ftp site have already
noticed this.
We've have already switched over to the accession.version definition line.
There are other places where this will become more apparent in standalone BLAST.
For example in blastdbdmc, if you retrieve sequences from our pre-formatted databases,
that is, those one directory up from FASTA, the default setting for returning FASTA will
spit out the new style format, accession.version.
You may see in my example command line that I am using an accession.
You can still use gi numbers to blastdbcmd, but you will get back by default this accession.version
format.
In Makeblastdb, it will accept both old- and new-style definition lines.
So you don't have to worry about changes things just yet.
It will also guess the source from the accession alone if you are using -parse_seqids; and
I assume that applies to our pre-formatted databases.
Also, many of you use the -gilist option to create a custom database for an organism or
taxonomic group.
That switch is still available and will remain available, but we also have a -seqidlist option.
That -seqidlist option will take accession.versioins.
Right now, -seqidlist is kind of slow with large lists, but it should be improved in
future releases.
We hope by the next release, but if not, the one after tha.
The next release by the way is 2.6.0 and as of today, that is scheduled to come out either
in December of this year or early next year.
Okay, a couple other changes.
In the default output formats, for those of you using the tabular output formats, you
are now going to get by default query accession, sequence accession as shown here.
In the next release, you will be getting accession.version.
You will not be getting back by default the gi style definition lines.
Those are the two major changes.
One of the improvements we have made is to offer another output format option and that
is output format option 18.
It will now give you a taxonomy organism report.
If you are familiar with using this on the web, it is similar in look to that.
It very nicely organizes the output by organism.
And finally in terms of improvement, we now have included composition-based statistics
when you use RPSTBLASTN.
If you are not familiar with this program, it allows you to input a nucleotide sequence,
then does the translations and searches the conserved domains database.
You get back conserved domains.
RPSBLAST allows you to input a protein sequence and see what conserved remains are there.
RPSTBLASTN allows you to input a nucleotide sequence.
I promised a couple of links.
You can go to our news page to find out about the general gi number phase out.
Go to our home page in the Develop section and the API section and you can read about
the switch to HTTPS.
For a full discussion of the release notes, go to the NCBI bookshelf.
You can just search NCBI bookshelf blast, and you'll get these release notes.
I am going to open this up for any questions.
I am going to check out our chat pod, here, to see if we've had any questions come in.
Okay.
We are not seeing any questions at the moment.
Thank you very much and we will see you at the next webinar.