Blast formatdb files

If for some reason you do want to create your own, note that the formatdb line-command is incorrect for protein indexes. Specifically, "-p F" indicates that the input file is in nucleotide format, not protein.

Most likely, the loc file path change is enough. Adjust my example to the actual path to the indexes in your directory structure. Heads up! This is a static archive of our support site.

Please go to help. If you want to search this archive visit the Galaxy Hub search. Log In. Welcome to Galaxy Biostar! User support for Galaxy! Question: Blast p error with database definition. Please log in to add an answer. Open Mobile Search. Off-Canvas Navigation Menu Toggle. Main Content. Syntax blastformat 'Inputdb', InputdbValue blastformat Arguments InputdbValue Character vector or string specifying a file name or path and file name of a FASTA file containing a set of sequences to be formatted as a blastable database.

FormatPathValue Character vector or string specifying the full path to the formatdb executable file, including the name and extension of the executable file. TitleValue Character vector or string specifying the title for the local database. LogValue Character vector or string specifying the file name or path and file name for the log file associated with the local database.

FormatArgsValue NCBI formatdb command, that is, a character vector or string containing one or more instances of - x and the option associated with it, used to specify input arguments.

Description Warning blastformat is not supported for macOS version Note To use the blastformat function, you must have a local copy of the NCBI formatdb executable file available from your system. Note If you rename the database files, make sure they all have the same name. Note The 'Title' property does not change the file name of the database files.

Note For a complete list of valid input arguments for the NCBI formatdb function, make sure that the formatdb executable file is located on your system path or current folder, then type the following at your system's command prompt.

Compatibility Considerations expand all blastformat has been removed Errors starting in Rb blastformat has been removed. References [1] Altschul, S. See Also blastncbi blastread getblast. Select a Web Site Choose a web site to get translated content where available and see local events and offers.

The Tax Blast link at the upper left of the graphic makes the chicken proteins much easier to identify. How many similar chicken proteins are there? What is the identity and E-value of the best chicken hit. We'll perform this search again using an advanced option to restrict to only chicken sequences later on. Jump ahead to this example. The BLink output shows a graphic depicting the extent of the alignment with the query P ; the BLAST raw score is linked to the Blast 2 Sequences alignment; the accession number is linked to the record in Entrez, and the gi is linked to the corresponding BLink output for that sequence.

The taxonomic distribution numbers in the boxes show that this signaling pathway is probably restricted to multicellular animals metazoa. Buttons at the top of the page allow you to sort your results in various ways. Click on the "Best Hits" button to see the best hit for each species. Click on the "Common Tree" button to see a phylogenetic view of the taxonomy of the organisms involved.

What two species of ray-finned fishes Actinopterygii have hits to Sma-4? In certain degenerative neurological diseases, prion proteins aggregate into polymers. Several of these prion diseases seem to be transmissible. Perhaps the most remarkable aspect of these is that the infectious agent appears to be an aberrant form of the prion protein itself.

Bovine spongiform encephalopathy BSE is one of the transmissible prion diseases that has received much recent notoriety. There are a number of polymorphisms that have been identified in the prion proteins for several mammals, notably human, mouse and sheep. Some of these are associated with inherited prion diseases and some with susceptibility to transmissible forms.

This is easier to see if you change the formatting options on the BLAST form to display one of the query anchored alignment options. Try the "flat query-anchored with identities" option. Set up this search. Understanding the effect of search space size on expect value. Jump back to the previous search. This time use the "Options for advanced blasting" and use an Entrez query to restrict to only chicken sequences.

You can enter the query in the left hand box by typing: Gallus gallus[organism] The following query also works: chicken[organism] C. This latter works because chicken is the accepted common name in our Entrez system for the species Gallus gallus. Simply typing the common name without the organism restriction won't necessarily give the same results. The Entrez help document provides details about formulating Entrez queries.

You can also select the organism from the pull-down list on the right. Compare the expect value of the best BLAST hit to the expect value obtained from the previous search of the entire nr. Is the hit more or less significant. For example: protein all[filter] NOT human[organism] Try the search with Sma-4 using an Entrez query to eliminate sequences from mammals. Jump back to the blastp search. You will need to increase the number of descriptions in the Format section of the page; increase to Position-specific information from a multiple sequence alignment of the sequences above this line are used to generate a position-specific score matrix PSSM in the next iteration.

Notice that one of the first proteins below this line is the Smad7 from the sheep Ovis aries. What is the E-value of this hit? Note that the Formatting page is refreshed in it's separate window , generating a new Request ID number. Click the "Format" button and the results of iteration 2 will load. Click on the "Skip to the first new sequence" link on the Iteration 2 results page. What is this sequence? What is its new expect value?