Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • maubp
    replied
    See http://seqanswers.com/forums/showthread.php?t=50017 for kaps's thread.

    Leave a comment:


  • kaps
    replied
    Originally posted by maubp View Post
    I think a separate thread would be a good idea for this question. See also http://blastedbio.blogspot.co.uk/201...-chimeras.html and http://www.ncbi.nlm.nih.gov/pubmed/?term=25428358
    Hello Maubp,

    Thanks for the blog links. i have also created a seperate thread as advised. its now called fasta files from NCBI

    Leave a comment:


  • maubp
    replied
    Originally posted by kaps View Post
    Dear all, In creating a local blast database, I downloaded fasta files from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ and http://www.ncbi.nlm.nih.gov/sites/nu...=%22Viruses%22[PORG]+AND+srcdb_refseq[PROP]. The former appeared larger than the latter, which of them is better? Do both both contain nr sequences? are they different?

    Thanks
    I think a separate thread would be a good idea for this question. See also http://blastedbio.blogspot.co.uk/201...-chimeras.html and http://www.ncbi.nlm.nih.gov/pubmed/?term=25428358

    Leave a comment:


  • kaps
    replied
    Dear all, In creating a local blast database, I downloaded fasta files from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ and http://www.ncbi.nlm.nih.gov/sites/nu...=%22Viruses%22[PORG]+AND+srcdb_refseq[PROP]. The former appeared larger than the latter, which of them is better? Do both both contain nr sequences? are they different?

    Thanks

    Leave a comment:


  • maubp
    replied
    The simple brute force solution is make a single merged FASTA file (e.g. using the cat command), and then build a BLAST database out of that.

    Leave a comment:


  • poudap
    replied
    Unfortunately the $(cat Strains/*.fasta) command did not work.

    The command space seperated also gave error:
    BLAST options error: File Sample_no2.fasta does not exist.

    Leave a comment:


  • maubp
    replied
    Originally posted by poudap View Post
    I am wondering if you could tell me how I can make a database from different files in batch?
    BLAST does not like this kind of command, where the second FASTA file is considered to be a positional argument:
    Code:
    makeblastdb -in Strains/example1.fasta Strains/example2.fasta -dbtype nucl -out db/stec_samples
    From past experimentation, I know it will work if you quote the list of filenames making them space separated (filenames with spaces are a problem):

    Code:
    makeblastdb -in "Strains/example1.fasta Strains/example2.fasta" -dbtype nucl -out db/stec_samples

    Leave a comment:


  • rhinoceros
    replied
    This might work:

    Code:
    makeblastdb -in $(cat Strains/*.fasta) -dbtype 'nucl' -out db/stec_samples

    Leave a comment:


  • poudap
    replied
    How I can make custom database in batch?

    I am wondering if you could tell me how I can make a database from different files in batch? The commands like entry_batch does not respond.
    I have also used below command but it gives the error stated afterwards:

    makeblastdb -in Strains/*.fasta -dbtype 'nucl' -out db/stec_samples

    Error: Too many positional arguments (1), the offending value: Strains/Sample_1.fasta

    P.S. A single database can be made from Sample_1.fasta with no error.

    Leave a comment:


  • ahmadsam
    replied
    Creating blastdb in windows

    after downloading and installation
    1-Use command prompt and go to the bin directory
    for creating a database like protein database you need a simple multi fasta file

    2- use this command :
    Code:
    makeblastdb -in D:\\ref.fasta -dbtype prot -out Plant
    with the above code makeblastdb generate 3 file with .pin , .phr and .psq format in the bin directory.
    Plant is the name of output database.

    3- for using this database in sample query :

    Code:
    blastp -query D:\\in.txt -db plant -out D:\\Out.txt

    Leave a comment:


  • rhinoceros
    replied
    Originally posted by utagenomics View Post
    Hey everyone,

    #I used the following to make the db

    makeblastdb -in supercontigs.fasta.txt -dbtype 'nucl' -out p.full

    #I then tried to run this the next step

    query=NGF.fasta -db=p.full -outfmt="6" -out=blast

    Any ideas how I can change my second step to successfully run the blast search?
    Well for one you haven't specified a program, which should probably be blastn in your case. Second, the correct syntax would be:

    blastn -query NGF.fasta -db p.full -outfmt 6 -out blast

    If that still doesn't work, then I'd guess that there are problems with your environmental variables. You could go around this by specifying the paths of your program, query file, and db, i.e.

    /where/is/blast/bin/blastn -query /where/is/this/fileNGF.fasta -db /where/is/this/db/p.full -outfmt 6 -out blast

    optional flag you should consider: -num_threads INSERT_NUMBER_OF_CORES_IN_YOUR_SYSTEM, e.g. -num_threads 2
    Last edited by rhinoceros; 04-29-2013, 05:33 AM.

    Leave a comment:


  • maubp
    replied
    Kyle - you've left out at least part of the command you ran, and more importantly you left out important details like what the error message was. That makes it almost impossible to guess what you've done wrong.

    Leave a comment:


  • utagenomics
    replied
    Hey everyone,

    So I am also having some similar issues. I successfully made my database in the correct folder, but then when I actually try to run my blast, it isn't working...

    #I used the following to make the db

    makeblastdb -in supercontigs.fasta.txt -dbtype 'nucl' -out p.full

    #I then tried to run this the next step

    query=NGF.fasta -db=p.full -outfmt="6" -out=blast

    Any ideas how I can change my second step to successfully run the blast search?

    Thanks,
    Kyle

    Leave a comment:


  • geneart
    replied
    BLAST database

    Yes, maubp ,you are correct ! I did setup the database using miRBASE mature.fa files .I was wondering if I need to format that datanase at all in doing that. It does not matter now as it worked. But I had another question again.
    I have short RNA sequences from Illumina sequencer and am trying to find matches in miRBASE through a blast standalone (which has mature.fa from miRBASE to be used as a database). Now when I directly use miRBASE and use SSEARCH I get hits however when I BLST locally I don't get any hits.
    I have used default parameters, which I would like to tweek to see if results change. My problem is how do I run BLASTN-short on cmd line or tweek the parameters in BLAST standalone? Any help? I looked up the BLAST manual that comes with the standalone but could not find it.
    I am not that command line savy so hoping someone can suggest ways of doing it ?
    Thanks in advance
    Geneart.

    Leave a comment:


  • maubp
    replied
    Hi geneart, I'm having trouble understanding your question. Are you saying you've downloaded a FASTA file from miRBASE and want to turn this into a database? If so yes, you should use the makeblastdb command.

    You can search directly against a FASTA file, but it is slower (and only uses one CPU), but will also give you pairwise e-values which will look more impressive than they really are, see:
    Sometimes using BLAST is frustrating. Today I'm writing about it returning different expectation values, and therefore different answers, de...

    Leave a comment:

Latest Articles

Collapse

  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 08:52 AM
0 responses
21 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
50 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-12-2024, 03:37 PM
0 responses
437 views
0 likes
Last Post seqadmin  
Working...
X