An Error By Using Ncbi-Blast-2.2.25+ (On Windows)
Hi all I downloaded blast+ software package (for windows), and installed like theBookshelf; to run it i used this "ncbi-blast-2.2.25+/bin/blastn –query text_query.txt –db refseq_genomic –out...
View Article(Determine If Necessary And) How To Realign Blast Results For Arlequin?
I am newbie in bioinformatics, and now trying to learn about alignments, so sorry about the lack of vocabulary. After blasting a sequence, this is my output from a BLASTN... lots of other aligns ......
View ArticleWhat does sframe signify in BLAST output?
Hi,I am relatively new to the field of Bioinformatics and have just been introduced to BLAST. I'm trying to understand the output available from the BLAST program. As listed in the NCBI manual, I am...
View ArticleHow Can Different 3 Reading Frames Have Similarity For The Same Sequence...
Hi, I have a DNA sequence ( it's about 388 bp), which I am comparing with GenBank sequences using Blastx. I understand that Blastx looks into all possible 6 reading frames when translating a DNA seq,...
View ArticleBlast Database Sequences Length
Hi allI am doing blast queries using genomes as databases. I would like to know if is possible to filter out database sequences by their length. So, if there is a sequence in the database that is...
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 ArticleIdentity Cutoff In Blast Output
I was wondering if there is any easy way to do an identity cutoff (e.g. Sequences down to 95% Id) from the blast output locally .I had a look at blastall usage options but haven't seen any flag (or...
View ArticleNCBI blast PHP API choice
Hello.I want to program a web application, based on PHP language. One of its features, will be the ability to send data and receive results to/from ncbi's server and then analyze them with other...
View ArticleIdentify short repeats in DNA sequence?
I want to identify the short repeated sequences in a given DNA sequence. For example, the sequence I have is atacctgcc ccc atacctgcc. The repeated sequence is 'atacctgcc'. Is there a program to...
View Articleblast FATAL ERROR: BlastFormattingInfoNew returned non-z
Hi,I'm running blast commands from a cluster of nodes and sometimes if succeeding and sometimes it fails.the command i run is:blastall -p blastn -g F -q -9999 -i...
View ArticleSEED assignment (MEGAN5)
For me it is not clear how MEGAN assign the SEED classes to the sequences. In the manual, it says that it is made throughtout the identification of RefSeq id (accession number?). When I load my blast...
View ArticleHuman Genbank Ids
I am working on a sequencing run that contains contamination. I did a de novo assembly and blasted the results against NR and filtered for the best hits. I now have a list of Genbank Ids. I simply want...
View ArticleBlastn / Tblastn : Mapping The Features Of The Query To The Hit.
I'm blasting+ (blastn+ or tblastn) an annotated sequence (a Genbank.xml sequence (nucleotide or protein) or an Uniprot.xml entry) against a DNA database.Is there a standard tool to map the features of...
View ArticleHow To Make Pssm With Makeblastdb
i want to make a pssm from a fasta file for searching with rpsblast, i have the 2.2.23+ version of blast, so formatdb is replaced with makeblastdb. I have used it to make a database from the genome im...
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 ArticleRunning A Standalone Batch Blast With Fasta File Using Perl, Can'T Get...
I'm running standalone blast locally. My blast query sequencess are in a fasta file called human_seqs.fasta, which comprise around 300 sequences. Being blasted against a much larger database called...
View ArticleMethod Of Getting Progress Of A Blast Run
Are there any parameters in blastall that'll make the program inform the user of the current progress of the blast run?
View ArticleNcbi Blast Command Line Align Two Sequences
I want to align 2 sequences using ncbi blast command line or bioperl script, I am new to blast and I found out that it compare a sequence to a database but what I need it to compare two sequences like...
View ArticlePerl Script To Check Top Blast Hits
I search for a perl script to check if the top BLAST hits to a query contained a full scientific binomial, i.e. for see if the next best hit has a complete scientific name with taxonomy, and to sorted...
View ArticleBlast2Go Memory Allocation
I'm running BLAST2GO on a Linux (Ubuntu 10.04 32 bit) machine with 24 GB RAM (8 processors). No matter what I specify for the maximum memory, it only allocates 455 MB RAM, which is not enough for the...
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