Makeblastdb Error In Blast+ 2.2.26
I am running makeblastdb from blast+ version 2.2.26 on uniprot_trmbl.fasta and get the following errorBLAST Database creation error: Error: Duplicate seq ids are found: GNL|BLORDID|2707210Any ideas...
View ArticleComparing Blast M8 Outputs
Hi,I want to compare BLAST outputs in m8 format to find out if any queries in the separate output files have the same subject hits to NCBI nr database.For example, for the 2 BLAST outputs in m8 format...
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 ArticleMakeblastdb Can'T Find My Fasta Files
I'm trying to make a nucleotide database for my sequences. After opening C:Program Files\NCBI\blast-2.2.28+> in the command line, I typed in makeblastdb -in test_gene.fsa -parse_seqids -dbtype...
View ArticleMegablast, Makembindex, And Choosing Nmers
I've been using MegaBLAST (in BLAST+) to test for high-similarity matches against hg18. It's exponentially faster than normal blastn for this purpose, but I'm not sure what settings I should use when...
View ArticleBlast output query
I did a local standalone blast pre-miRNAs against a genome in tabular format (-m 8) and got the results. My next steps for refining the results include GC content analysis, RepeatMasker etc. I am...
View ArticleBlast+ Error
hi，everyone！ I use blast+ to make annotation of RNA-seq data against nr. When I run blast, it always stopped by error. my command line is "blastn -task blastn -query Unigene.fa -db human.rna.fna -out...
View ArticleE-Value In Blast
Hi all:I am calculating my e-Value for my own BLAST alignment. I used the formulae: e= mn2^-S'where: m = length of the query sequence n = total number of lengths of all template sequences in the...
View ArticleBlast Results: Xml Tags Explained ?
Hi there,I would like to know if there is any description of the tags that are found in the XML file generated by blastall. I just cannot find any comprehensive document on the web .More precisely, I...
View ArticleHow to understand which DNA strand is (5' to 3' ot 3' to 5') in the result of...
Hi!if a have such a result from a blast run, how can i understand if its in the 5' or 3' side of the DNA or protein strand ?> gnl|SRA|SRR456295.4505.2 FIHSSUW02H237H.2 length=250 Length=250 Score =...
View ArticleGenomic coordinates from GI accession numbers
I have a list of GI accession numbers that I obtained following a protein BLAST search. These are from different bacterial genomes. I've pasted some examples below. 108765232 108769511 108769512...
View ArticleCreate a custom .gtf file with a list of genes
Hi GuysI am new to the RNA Seq world and just starting out with linux. I need to create a custom gene annotation file with a list of genes I am interested in analyzing. How do I do that.
View ArticleHow To Identify Proteins Present Only In Pathogens But Not In Non-Pathogens...
I used PSI-CD-HIT-2D to compare the proteome of pathogen A to pathogen B from the same genus at 30% identity. The matched protein sequences (homologs above 30% identity) are then compared again to...
View Articlestart and stop position of mapping in Blast
I used makeblastdb to search many short fasta sequences in a known organism. I successfully completed this step and got the mappings. My question is1. how can I get the start and stop coordinate ?for...
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 ArticleBlast2Go Statistics
HI When I run blast2go I want to receive statistics about how many sequences fit to each category. When I go to statistics in the blast2go I only manage to generate graphs. How can I receive the data...
View ArticleExtracting Fasta Alignments From Parsed Blastxml File
Hello, I have cobbled together a small script that parses a BLASTxml file. It seems to parse the xml file just fine (judging from what it prints to the screen). The problem is the hsp.fas alignment...
View ArticleHelp In Configuring A Local Blast Server.
Hi all.I am attempting to configure a local BLAST server on a Windows XP machine. I found the following series of explanations helpful but incomplete:http://www.ncbi.nlm.nih.gov/books/NBK52637/Relevant...
View ArticleMake A Dotplot From Blast Alignment
Hi all,I am a complete beginner with blast. I used the NCBI online service for aligning two sequences, and got a nice dotplot representation. Now I am running blast on my pc, and I would like to obtain...
View ArticleCreating A Dna Sequence Database Locally For Blastplus
Hi,I have a fasta file containing cDNA sequences and I would like to create a blastable database for blastplus, (using blastn) that I have installed locally. I am, however, unsuccessful up to now as I...
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