The compressed files of pre-formatted blast databases must be inflated with gzip or other decompress utilities. The working database files can then be extracted out of the resulting tar file using tar program on Unix/Linux or WinZip and StuffIt Expander on Windows and Macintosh platforms, respectively.

Edit: the decompress option is not documented in the ncbi book, but is present in the source code, since 2.2.22+ also in the latest windows version, but not in 2.2.18+ - 21! so the following should work update_blastdb.pl --decompress refseq_rna unless you have a very old version of blast, and indeed works for me, if your version is too old you should update.

Update_blastdb.pl Download Database

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Yes, I also see it in the source code on the ncbi site. The source code of my local update_blastdb.pl is different. Is it save to copy the content of update_blastdb.pl on the website to my local one? I really need to decompress.

I actually have the latest version of blast+. It does not include the decompress in the update_blastdb.pl. Can I just replace the source code of update_blastdb.pl with the one have decompress option? is it save?

The latest version for windows is 2.2.31, I have checked the source and it contains the parameter. Which version do you have? I guess that you have an old script left over in the installation directory, the latest script has the following commit information:

I'm getting an error when running the updateblastdb.pl. I do perl update_blastdb.pl and get the error that perl docs needs to be installed, so installed it but now when I do the same command I'm getting a different page giving me options. So no I'm using perl update_blastdb.pl -showall blastdb and I get the error "use of uninitialized value $retval[0] in concatenation (.) or string at updateblast.db line 110. How do I run this script to download the BLAST database?

I tried with the est_mouse database. I did perl update_blastdb.pl est_mouse. and got the error est_mouse not found, skipping. The same happened with nr, I tried your exact line. Im running on Ubuntu 12.04 in virtual box, would that be the cause of the issue?

That's strange. I just started the est_mouse command and it seems to be running fine.It also works okay on my 12.04 Ubuntu bare install (just tested), but it seems like it is failing in the virtual image I just spun up (vanilla install of 12.04). I am not entirely sure what is going on.

Although it has been a few years. I ran into the same issue! I am not used to windows and installed blast under C:\Programs. What I didn't know is, that under windows you will never be able to set write-rights in this directory on a specific script. Just run the script in a different directory other than C:\Programs.

It has been roughly 6.3 years since this was posted, but in case you or anyone is still wondering, I think your issue is the use of the perl command at the beginning. with the installation of BLAST+ the path to update_blastdb.pl is likely added to the PATH variable. The perl command takes a script in the current directory and runs it, however, the update_blastdb.pl document can be ran without the use of perl (as it initiates perl by itself already). therefore you can run the following

It is worthwhile realizing that the blastn command must be ran from within the directory where the database is saved. If only the path is specified blastn will not be able to output taxonomic / scientific names.

Now use the perl script to download the database of your choice. The decompress option automatically decompresses the tar.gz files. Depending on what database you choose to download and your internet speeds, this could be a lengthy process.

I recently download the nr files from ncbi ftp using the update_blastdb.pl script. When I try to run blast, i got an error telling I need a nr.pl file. I just tried to use makeblastdb to create the file using (makeblastdb -dbtype prot -out nr -title "non-redundant") but the script doesn't seem to work. can anyone tell me how to index those files or where to find the nr.pl document?

Yes. The update_blastdb.pl program is a part of the BLAST+ command line suite of applications and can conveniently download the BLAST databases. We have updated the version that accompanies the BLAST+ 2.8.1 executables (January 2019) to support Accession-Based BLAST databases. There is a new parameter for update_blastdb.pl called -blastdb_version which allows you to set the version of the databases to which you wish to update.

The table below shows some of the available BLAST databases via this method (subject to change without notice). To see all available BLAST databases, please run the command update_blastdb.pl --showall --passive.

Before we start, make sure you went over your bash notes, since we will be using several of the commands we saw in prevoious tutorials. Despite I will touch briefly on the web-based blast, I am assuming you know the basics on how to make blast searches on the BLAST website.

Log in into your Compute Canada account, create a folder for this tutorial (e.g Blast_tutorial), and open an interactive shell with salloc as we explained last tutorial with 2GB of memory. in the terminal type (remember to change the account for your own group if you are not in Cristescu lab):

BLAST or Basic Local Alignment Search Tool, is an alignment service available at NCBI. As its name exlpains, this software aligns a query sequence (your sequence) with the database sequences, and returns the closest match to your query. It does this in 4 steps (images from Alarfaj et al.):

blastn stands for nucleotide blast. It has two mandatory arguments which are -query (the fasta file) and -db the database where to look. Our first seach will be as follows (I added the optional -num_threads which makes it faster):

Now we have a very verbose help, where we can see that -out allow us to redirect the output to a file. This will become handy later on when we want to manipulate files without writing all intermediate files.

The format of the output file is parwise (check the help for formatting options). You can change the formatting by passing numbers to the -outfmt option. Looking at the help we see that the options are:

Now we have only 5 alignemnts, although the report still contains everything < 1e-115. This is because the report have full descriptions that can be controlled with num_descriptions. Note that num_alignments and num_descriptions are not mutually exclusive, but cannot be use with -max_target_seqs:

I have almost high quality Illumina reads that were trimmed and assembled using CLC genomic workbench software, I tried different K-mer size and got the best assembly, in terms of some basic parameters, like N50, the number of contigs and the percentage of mapped back reads (about 90%) in K-mer of 64. This assembly (44.8 MB in size) was subjected to cd-hit tool with strict 100% identity for the alignments since plants have many paralogues with have high sequence identity, but, the size of output file has not been changed. I also tried this analysis with stringency of 0.9, and the output size file (43.5MB) did not change significantly as compared with the original input file (44.8 MB). Could anybody please let me know whether these results are usual or there is something wrong? Thanks for any comments

I'm using biopython to BLAST over the internet. However, it only saves 30 results (there are more than 30 results that are under the e-value I chose) in the xml. I've been looking all over but can't find how to make that number higher. So my question is, how can you show more results from BLAST using biopython. I'm using NCBIWWW.qblast from BIO.BLAST.

I now have excel spreadsheets with only the genes/Isoforms present in these conditions with transcript id and expression value... I want to BLAST these against RNA-seq databases. Is there a program which lets me merge the filtered sequences with my Trinity.fasta file or am I thinking off track and is there another way to simply do this?

Just wondering if you guys have come across or developed any process to check for contamination in PacBio reads. By contamination what I mean is to align/blast the PacBio reads to some reference like (nt, 16s etc) to see if proportion of reads hit something not expected pointing to a possible contamination.

hi , i'm using biopython to parse my blast xml outputi make condition print on the number of for query.i print my query and sbject if the query have only one hit.but it's not workinghere is my script please help. thanks

This isnt my usual way if doing things but because im using Plone it has to be done this way.The function below takes a variable "x" which is the query sequence. Its is then formatted to a blast-able format and then blasted against the database. When results are retuned the file is empty. Any idea why? I had this working but now its not...

and it connect to NCBI successfully and download swissport in the bin folder. So, now I have two swissprot.tar.gz. One I download it in db folder and one downloaded in bin folder after running perl cammand.

Hi, I'm a biology student and i'm using Blast for the first time in my life. I have make a similarity searching between my query, human cox4, and mammals genomes. If I select in Blast parameters, "organism: mammalia" and I also select "exclude", I won't have mammals entries?

I typed %f so that it's in Fasta format, and even after spending so much time on the internet to figure out, I still have no idea what to do for this error.. Would you please be able to help me out? Thank you so much in advance.

I'm a student and i've got to make a paper about bioinformatics i've been working on it for a while and i'm almost done.I only have to write about BLAST, YASARA and the huntington disease approached by bioinformatics research.I'm having some difficulties with those three chapters. If there's anyone who would like to help me, please send a message.

Also one one more question. Is it possible to run blast with just nr.00 and nr.01 and not having whole database dowloaded? I tried tu run it, but I got error that he is missing nr.02. Is there a way to tell him that my database is just two nr arhives long? 152ee80cbc

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