Local Mirror Of Biological Databases
I'd like to set up a local mirror of certain large databases like the nt BLAST database, interpro etc.The biomirror project looks like a good candidate, but they seem to advocate using GridFTP, and...
View Article[Fastacmd] How To Retrieve Sequence From Blast Db
Let's say I have multifasta with protein sequences having internal IDs (integer)>1234 MGKL...*I build blast db using:formatdb -i infile.fa -pF -n someDBBut then, I'm unable to retrieve sequence from...
View ArticleWhy Does Blastdbcmd Produce The Error: Oid Not Found
hI,,,I am trying to extract fasta sequences from a local db using blastcmd command (NCBI BLAST) as follows blastdbcmd -db blastdb/9311 -dbtype prot -entry_batch 93hmmsearchacc.txt -out vivien.fastaFor...
View ArticleStarting Point
I am trying to get into bioinformatics or just trying to get a jist of what is going on. I wanted to see the difference between different methods for gene variation. I looked at blast and installed it...
View ArticleStandalone BLAST with kingdom classification
Hi all,I have an assembled transcriptome from an organism hosting various symbionts and I'm now interested in how many of my contigs hitting to the different kingdoms. What I've found so far is the...
View ArticleHow To Blast Kegg-Only Data In The 'Nr' Database
Hi there,I dont have a locally KEGG database bought,but I want to Blast my sequences against only the KEGG part of nr db cause you know blast whole nr is really time consuming.Here is my...
View ArticleHow To Blast A Sequence Against Multiple Databases
Hello,I have downloaded all the chromosome of Bos taurus and I have changed them in blast format using makeblastdb..and now I want to locally blast my sequence against these all chromosomes. now I have...
View ArticleHow To Get Ungapped Sequences From Blast Output?
I am interested in getting ungapped sequence hits (hspsnogap) from blast output, I tried using this:result_handle = NCBIWWW.qblast("blastp", "nr", record.format("fasta"),expect=10,"hsps_no_gap")...
View ArticleFormatdb From A Batch Of Fasta Sequences
Hi I have a batch of fasta files, each one is a file of ESTs from a different plant. I want to create a database for all the plants, how can I use formatdb (or another way) to create one database which...
View ArticleIs There Such A Way/ Program To Do This...
Hi guys,I followed the Trinity/ RSEM/ EdgeR pipeline and have produced some FPKM spreadsheets for genes and isoforms.I am currently analysing the isoforms:I have 3 sample conditions and I am comparing...
View ArticleHow Can I Batch Blast Sequences To Identify Them?
I have a list of 189 Accession numbers for 16s rRNA, how can I batch BLAST these to find which species they are closest too? I tried this server: http://greengene.uml.edu/programs/NCBI_Blast.html but...
View ArticleMakeblastdb Help
Hi,I feel I'm being really dumb here, so please excuse me! I have a file of fasta sequences which I want to make into a blast databse for standalone blast.I haev the fasta file saved in the bin folder...
View ArticleMissing BLAST hits - max_hsps and max_target_seqs?
Hi, I have a single file that contains 10,000 query sequences, each 300bp long. The subject is a single chromosome that I have imported into a nucleotide database ("makeblastdb -dbtype nucl"). Due to...
View ArticleBlast Help On Nucleotide Collection Nr/Nt
I am running a local blast server. I can format and blast my own databases. However, I am unsure of how to setup the "Nucleotide collection nr/nt" database from this NCBI Blast URL. Can I just download...
View ArticleProblem with NCBI-BlastN
Hello, I have recently reinstalled the OS of my workstation, changing from Fedora to Ubuntu. I then proceeded to install ncbi-blast (in its 2.2.28 version), but oddly when I try to run a job, it only...
View ArticleHow To Downlad Blastall Executable
Hi,It seems that the old version of blast (blastall) can make use of multithread processing and speed up things whereas new blast+ versions get stuck to using single thread even when you set the...
View ArticleHow To Acquire A Pssm Of A Protein Fasta With Ncbi-Blast-2.2.29+
I am a newcomer to ncbi-blast-2.2.29+. Previously, I had been using blastpgp to gain PSSM. In blastpgp, to gain a PSSM of a protein fasta, I ran command as follows:blastpgp -a $BLAST_NUM_CPUS -t 1 -i...
View ArticleLooking For Frequency Of A Very Specific Rna Editing Event In Publicly...
I am working on a ubiquitously and well expressed gene whose ~1.5 kb-sized transcripts get mutated at one and only one site. The mutation is a nonsense one that changes an ORF codon of the mRNA to a...
View ArticleAny Way To Ncbi Blast Multiple Protein Sequences?
Is there any tools or any direction anyone can point me in towards Blasting multiple amino acid sequences on http://blast.ncbi.nlm.nih.gov/Blast.cgi ?I could potentially write a script to do this and...
View ArticleIs Blastall Only Using Blast, Not Blast+?
Hi all, is blastall using BLAST but not BLAST+? If no, then how do I check which BLAST (+ or not) it is? Thanks in advance.
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