Human 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 ArticleDatabase Error When Running Blastn
Hello, as initially stated here, I am experiencing problems when I try to run the blastn command blastn -query myquery -db mydatabase.fasta.nhr.What I get is:BLAST Database error: No alias or index...
View ArticleBlast 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 ArticleBlast+ Stand Alone Version For Sequence Alignment
HiOn the on line version of Blastp (link text) there is a sequence alignment section (and it produces E-values for the alignment).and now I want to use the standalone version to perform alignment(My...
View ArticleDistribution of e-values in Best Reciprocal Blast Hits for Ortholog Mining
Does anyone have an idea of how the distribution of expect values will look when using reciprocal blast to detect orthologs?
View ArticleQuery Vs. Target Using Blast2
I'm running blast2 locally using DNA sequences in fasta files. I have one large target and a load of smaller query sequences.Version: 1.2.2.21.20090809-1 (blast2)blast2 -p blastn -r 0 -q -2 -G 2 -E 2...
View ArticleFind The Rid For A Remote Blast+ Result
I ran a remote blastn search using the command line blast 2.2.25+ and got the results back in asn format. when I went to reformat the results using blast_formatter, I realized I needed the RID for my...
View Articlelocal or remote blast BLASTp against pdb database (formatdb)
I want to blastp protein sequence file (>3000 sequences) against PDB database for generating templates for Homology modeling. Please help!!I tried remote blast and local blast using formatdb but...
View ArticleWhat'S Faster? "Blastall -P Blastp" Or "Blastp?"
I am just wondering if anyone has done a timed test and/or a memory test with blastall compared to blastp. In other words, classic BLAST vs BLAST+. It'd be really interesting to get some kind of...
View ArticleHow To Build The Correct Blast Url For The Rest Interface
Hi All,I am having difficulties constructing a BLAST query via the REST interface. In particular I would like to have a defline via QUERY_BELIEVE_DEFLINE and actually submit two sequences. The URL I...
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Configuring Path To Point To The Bin Directory Inside The Ncbi Folder After...
I can't seem to get Terminal to accept the syntax described on NCBI's help page regarding configuration of the standalone BLAST installation. Here's my syntax and the error messages:
View ArticleThe Same Sequence Occurs Multiple Times In Blastp Output
Hi there,I am using blastp (using blast+ 2.2.25) to align bacterial proteins (in the file multiple_queries.fasta) against a custom database (genome.db) containing all proteins coded by the genomes of 6...
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 ArticleHow To Merge Contiguous Blast Hsps! (-M 8 Tab)
Hi, guys! I performed blastx (-m 8) using a query file of many sequences, and for each target sequence, the output contains many fragmental hsps of significance, and these hsps have overlap positions...
View ArticleNcbi Blast+ Taxid And Taxid_Map
2 related questions. How does the -taxid argument for the NCBI's blast-2.2.24+ makeblastdb command work? When I execute:makeblastdb -title "BO" -dbtype nucl -out BO -in BO.fna -parse_seqids -taxid 3712...
View ArticleBLAST: Is there a difference between splitting queries and using more threads?
Hi,I'm wondering:if I want to blast a large number of protein sequences against the ncbi-nr database (say for example in order to analyse the species and function composition with MEGAN), which of...
View ArticleProtein Sequence Alignment
I want to know how to call Blast from java code, I have wildtype residue, mutant residue, position of mutation, and protein sequenceI want to calculate the frequency of wildtype residue, mutant...
View ArticleHow Long Should It Take To Make A Blast Database?
HiI'm trying to install a local copy of polyphen and one of the stages is to make a blastdb from uniref100.I ran this command last night and its still going nearly 12 hours later. I don't know if this...
View ArticleCommand to get BlastDB(Blast Database) information
Hi guys, I have a very simple question on how to get the information on the size of BLASTDB created using standalone BLAST. I have created several BLAST databases and now I need information on their...
View ArticleHow to remove redundant and poor quality ESTs
Hi community, i have a question that, How to remove redundant and poor quality ESTs from whole data set through online .......?
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