Command blast excluding species
Hello,When using NCBI's interface I can exclude species, genus, even phyla. Is there a way to do that in command line blast?I need to exclude one species from my search. I see this can somehow be done...
View Articlebioinformatics related problems
hello friendsi have downloaded blast database (rpsd; for conserved domain). but i am unable to us it. so plz can anyone tell me how i can use (untar files of cdd.tar.gz file).thanks:)
View ArticleScript Or Tools To Blast Primer Sequences Against Fasta File
Hi, I am looking for a script or tool to blasta all of my primer sequences against the reference fasta sequence. When i tried to use megablast i did not get any output eventhough those primers are...
View ArticleGet Snps, Indels From Biopython Blast Parser
Hi all,Is there a way through the bioPython API to get the list of variants from BLAST alignments?I have done my alignments using standalone BLAST by providing -query and -subject, and the output is...
View ArticleHow update Blast+?
how i can update Blast+?, because i have the 2.28 version, and i wanna update to 2.29 version, but i dont know if i need to download and install, or i need to unistall the previous version, or if exist...
View ArticleObtaining alignment from psiblast
Hi everyone,I am using stand alone version of Psi-blast. I want to get just the query sequence followed by matched-hit sequences (both aligned) in fasta format.How to do it in Biopython or stand alone...
View Articledata from SRA against blast databases method.
Hello.I want to find a specific gene inside SRA files and I am wondering if i am using a correct way to align those sequences because its the first time that i am "playing" with something like that.So,...
View ArticleProtein Sequence Alignment Using Blast
Hi All, I am trying to run Blast over protein sequences from two organisms. I downloaded the fasta from NCBI. I am trying to iterate over the list of sequences in the fasta file and do a sequence...
View ArticleDetection of viral nucleic acids in metagenomic aDNA samples
Hello there,at my Institute we are now aiming at detecting viral nucleic acids in metagenomic aDNA samples. As a guy who is totaly new to all the bioinformatics stuff at the moment I'am just looking...
View ArticleNcbi Blast Output Missing Subject Name
I'm wondering if anyone has stumbled upon this issue I'm having with blast. I have a set of contigs I'm blasting against NCBI's NR blast database, and the blast report I get back has a blank field for...
View ArticleNo hits found
Bioinformatics noob here,Im working with a firefly database. I have downloaded the blast executables and made a local database with the makeblastdb command. To test the database I have used the blastn...
View ArticleGenerating .xml file from list of genes using BLAST
Hello,I need to generate an .xml file from BLAST starting with a list of genes (currently in .txt format).Do I require a script to do this, or is there an easier way to do this directly on the online...
View Article本地Blast的输入和输出问题
在这里学习了本地blast的使用，但是有个问题，本地blast默认的是标准输入和标准输出，由于需要，我希望将序列通过变量输入并且将比对结果输出到另一个变量。 比如 $reference中是一条序列（不是从文件读入） 而将结果输出到变量$blast_result（不是从文件读入）但是用如下脚本是无法实现的 my $localblast=system("$blastall -p blastp -d...
View ArticleBlast Params : Word Size, Gap Existence, Extension Penalties
I have just started Biopython and require some assitance. Using 'NCBIWWW.qblast' function (or any other); how can I set the word size and gap existence,extension penalties for BLASTp? Thanx in advance.
View ArticleHow Can I Automate Blast Of >1 Sequence And Output The Top Hits For Each Input?
I'm looking for a way to do BLAST simultaneously with >1 sequence. The input is several fasta files or one file containing several sequence formatted in fasta. For an initial testing, I want to try...
View ArticleUsing Biopython and BLAST+ to automate de novo viral contig sorting
Hello all, I need some assistance in programing a script to run a basic nt BLAST on contigs and then save the requested files in a output file (csv) for easy sorting. I have an understanding of python...
View Articlehow many RAM and CPU are required to perform comprehensive NGS analysis?
Hi all,Please provide me how many RAM (GB) and CPU are required to perform de novo transcriptome assembly for about 400 million paired-end reads (using trinity) and subsequent analysis, especially...
View ArticleEmbedding Blast Tool In A Website
I'm planning to include BLAST search tool in a website to search against my own databases where user can choose one of the two databases with all the optional blast parameters (e.g. E value cutoff,...
View ArticleMaking Specialised A Local Blast Db
Hi,I need to make a local Blast DNA (nt) database that only includes sequences from plants. I'd also like to make one with only chloroplast sequences. Put I can't find any tools to do this. I don't...
View ArticleFinding The Gene Annotation Output From Web Blast In The Xml Etc. ?
Hi, I'm new to bioinformatics and am still learning how all the public databases interconnect so please bear with me :) I have de novo assembled a set of bacterial genomes, located and extracted...
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