Blast Nucleotide Vs. Nucleotide, Plus-Minus Results Only
Hi Folks, I am interested in running a blastn search to search for complementary sequence (potential biological function) between two groups of sequences, (Query blasted against Reference) such that...
View ArticleDna Sequencers- Required Matching Errors For 150 Bps
I am doing some experiment using BowTie and WHAM which are short read aligners that aligns short DNA sequences (reads) to the human genome like BLAST. In WHAM, it is specified that for 75 bps reads, it...
View ArticleWhy Is Makeprofiledb Throwing Confusing Defline Errors?
I have an alignment file [alignment.aln]:>lcl|21974 MRLQLILTITLLLTSFMGYRDAAVIQGKTERSAMKMRKLLQILHKNSCGCNDDDSDGDDCCFGTCLDNACWPVKKRSSAII can make a blastdb with this file:makeblastdb -in alignment.aln...
View ArticleIdentifying Clone Sequence Proteins
When conducting a Large Y2H screen to find potential interactions for the HIV-1 MA protein. A number of the clone sequences identified cannot be ascribed to a protein using preliminary BLAST. Do any...
View ArticleTrying To Extract Blast Results Into Xml Outfile From Larger Blast Xml File
This is probably a fairly basic question, so I apologize in advance, but I can't seem to figure out how to output xml format using Biopython. Basically, I have a fairly large BLAST results file in xml...
View ArticleGenomic Sequences For Drosophila In Refseq
Pscan was recommended to do TF enrichment previously. RefSeq (for human, mouse, and drosophila, e.g. NM_000546) in one of the acceptable identifiers. I have a list of genes in a non-model organism, and...
View ArticleGenerating Protein Consensus Sequence For Blast Input
I have a set of 3 protein sequences for which I need to find the "consensus sequence" which can be used as an input to blast against a local database.how should I go about it?
View ArticleBlast2 Vs Ncbi-Blast+
In my debian testing system I have two blast packages:ncbi-blast+ 2.2.25-7 with homepagehttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/and blast2 1:2.2.25.20110713-3 with homepage...
View Articlegetting error in runing tblastn
Hello group, i am trying to run tblastn of version 2.2.26+ for mapping peptides on eukaryotic genome, i am running the command tblastn -query sequence.fa -out output.txt -subject ref_protein.fa -evalue...
View ArticleIs Blast+ Running As Fast As It Could ?
Hi all, I am trying to run a tblastn search of nt locally using blast+2.2.25, and was wondering if anyone new if it's going as fast as it should - I have 1000's of queries to get through! I should...
View ArticleDoes Blast Use Multiple Sequence Alignment
does blast database search use multiple sequence alignment technique ?
View ArticleBlast E-Value To Database Size
Hi,I'm thinking of splitting the database to smaller chunks. And, blast my sequences against them each on a separate process. My only concern is the results (which I will merge later).Would the...
View ArticleBlast For Cygwin?
Which version of BLAST is prepared for Cygwin?I tried to compile ncbi-blast-2.2.26+-src.tar.gz under Cygwin 1.7.13. The compilation stopped at "checking python" at first. After python was installed,...
View ArticleRepeatmasker Crashes Before End Of Run With "Can'T Fork..."
I've been trying to run RepeatMasker but it keeps crashing with the error "Can't fork...". In the RepeatMasker script source code, this is here:FORK: { if ( $pid = fork ) { $flag = 1; waitpid( $pid, 0...
View ArticleBlastp And Biopython
I have noticed that when I blast my own database in particular some of the sequences get truncated. This is using my local blast algorithm.For example I know that the sequence FYNTSTPQ and FYNTSTRR...
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 ArticleWhat software to use to map and observe substitutional patterns across...
I have protein sequences from about 50 species which I want to align and observe/retrieve key (functionally interesting) sites. Apart from using Blast (blastp) to align sequences and view query...
View ArticleBlast Alignment Bug
I tried to find a short oligonucleotide sequence (probe) in a transcript and I knew for sure that the transcript contained the probe. But the latest version of the BLAST stand-alone algorithm (2.2.25+)...
View ArticleBlast+ Error Code=12
Something really bizarre is going on. I ran 6 tblastn jobs independently using the following command line entry: tblastn -query blastqueries14920.fasta -out blastqueries14920.fasta.out -db...
View ArticleTurn Off Blast Search On Reverse Complement Strand In Blastn
I have a quick question: How can I turn off search on reverse complement strand of my query nucleotide sequence in blastn?For example, I don't want 'GUAAAGCCAAAUCUUCGGUUA' to be a hit when I use...
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