Makeblastdb 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 ArticleGiven Sequences, How To Compute A Low Complexity Score For Each Sequence?
Is there a way or a program/module that I can use to compute the complexity score for the given sequences? I want to rank sequences by their complexity.
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 ArticlePipeline Or Tool For Going From Assembled Genome Fasta & Gff Files Directly...
I'm hoping this doesn't come off as a lazy question, but I am wondering if anyone is aware of a tool or pipeline out there that directly takes reference genome (supercontigs, contigs, scaffold, what...
View ArticleHow To Concatenate Blast Results (M8) Via Setting Threshold Of Distance...
hi, dear guysI performance blastn (-m 8) using a query file of many sequences, and for each query sequence, the output contains many fragmental hits of significance. however, these hits have no...
View ArticleStandalone Blast Options
Hi all , I'm using local BLAST to retreive the single top most hit invoking "-v" option of blastall/RPSBLAST, from the local database sequences. I'm getting the top hit in most of the cases but in some...
View ArticleBlastx For A Million Metagenomic Sequences
I intend to use a similarity based binning program like MEGAN or SOrt-ITEMS or CARMA for analyzing sequences in my metagenomic data set. For this, I first have to generate a BLASTx output of my...
View ArticleBlast Two Sequences
Hello all! I have a list of pairs of proteins and I want to compare speed and accuracy of "BLAST Two Sequences" to a Smith-Waterman program for alignment. I know there is a "Blast Two Sequences" option...
View ArticleBlast Gives Cryptic Errors
I have a list of proteins in fasta format (say goodProteins.fasta). I first make a compatible database using NCBI's formatdb v 2.2.18:formatdb -i goodProteins.fasta -p T -o TThis gives me a number of...
View ArticleLocal Blast Returns No Result, While Using The Website There Are Some Matches
I want to blast some EST with local blast. However, for some sequences, there are no matches while with the website http://www.arabidopsis.org/Blast/index.jsp.(I download the database from the site,...
View ArticleGet Blast Database Size
I have piped unknown length sequences into makeblastdb. Now I want to know total length of those sequences (BLAST database size).Example: # "cat" is used as an example # My "real" sequences are piped...
View ArticleStandalone Blast 2 Short Sequences
Hi. I'm new to blast. I have downloaded blast+ and installed on a windows machine. I want to use blast to align short nucleotide sequences (<400 bases) A against reads of similar length B. Set A and...
View ArticleAny Local Gui-Guided Blast Tools?
Hi All,I am currently looking into local, GUI-guided BLAST tools. I stumbled upon BlastStation2 and was wondering if anyone has experience with it ? Are there any similar tools such as BlastStation2...
View ArticleUsing Blast From Within Perl.
Hi all.I recently installed the latest version of Blast (standalone) on a Win XP machine and altered the appropriate path settings, i.e., C:\blast\bin. Having searched the web for an example of using...
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 Article[Ncbi-Blast-2.2.28+] Thrownullpointerexception() When Running Blastn
Hello, I'm still rather new to blast+ and I'm trying to get an implemented tool to work locally(that already works somewhere else). The tool just completely skips blasting and doesn't even show me any...
View ArticleSetting Up Blast Server
Hi, i'm trying to set up my own blast server for convenience and i'm having some technical issues which might not be purely bioinformatics related but i hope someone here has done it before.My problem...
View ArticleA Tool For Flagging Blast Searches?
I want to know if there is a blast way or a blast-like tool in which a query will search through a database and return only predetermined hits based on given flags like sequence fasta ids. To be more...
View ArticlePsiblast Fasta Formatted Output
Hi,I have a FASTA formatted protein sequence (stored in DsbA.fa) and I would like to use PSI-BLAST (not the web server. The command line in the BLAST+ package) to generate hits. I am using the...
View ArticleBlastdb_Aliastool Error
Hi everyone,I would like to build a human+bacteria+archaea subset of the nr database. So what I did is:Get the nr databaseGet the GI list of human+bacteria+archaea from Entrez Protein databaseUse this...
View Article