Average nucleotide identity
Hi,I'm using ANI to determine if two bacteria species are related or not. What is the threshold for saying two sequences come from different species ?
View ArticleIs It Possible To Get Near Global Alignment From Blast?
Hi to all When a query sequence identical to a database sequence is done BLAST, the alignment is shown for 100% of the sequence ie.complete coverage. Cannot this situation may be said global alignment?...
View ArticleBlast The Sequences Obtained From Translocations To Get Their Positions
HI I have a file that contains information like this:Gene1 Gene2 sequence FOXP1 ABL1 acacctctcaatgcagctttacagCtctacgtctcctccgagagccgctgtggagagttacgtcgaaatgtc FUS ATF1...
View ArticleAre Alignment Lengths Reported In Ncbi Blast+ Results Counting Nucleotides Or...
Very simply, what are the units of the alignment length reported by BLASTX and BLASTP? The units of length are not listed in the output column headings (-outfmt 7) and I have found nothing in the...
View ArticleProblem using a custom blast database in tblastx
Hello. I tried to create a custom DB for blast. I downloaded fasta files from NCBI from an SRA project and then run this command makeblastdb -dbtype nucl -in sra_data-DB.fasta -input_type fasta -out...
View Articlecareer for bioinformatics in USA . are there any job opportunities for a...
hello friends ,I've completed my b tech biotechnology . i have plans to do my masters in area of bioinformatics in USA .Can any one pl tell me hw was the carrier for a bioinformatic student in usa...
View ArticleHow to curate my BLAST results
Hi I've been trying to design a primer from the 16S gene sequence of leptospira, to detect any species of leptospira in the isolate ( as the 16S gene sequence is highly conserved ) and BLASTing the...
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 ArticleProblem with NCBI-BlastN
Hello, I have recently reinstalled the OS of my workstation, changing from Fedora to Ubuntu. I then proceeded to install ncbi-blast (in its 2.2.28 version), but oddly when I try to run a job, it only...
View ArticleLocal Blast: Querying A Single Sequence Without Input File. Possible ?
Hi,When using BLASTALL by command line, is there any way of querying BLASTALL without using any input file but a directly a sequence ?I would like to do something like:blastall -n blastn -d MyBud.fna...
View ArticleMEGAN5 - input blast -m8 option problem
Hi, I am trying to run MEGAN5 using a blast table generated by an associated researcher. I know that MEGAN is able to interpret blast files fomatted by the m8 option. I have tried to load the tables...
View ArticleAny tool to generate protein similarity matrix
Hi, I want to calculate the similarities between each protein pariwise and then implement random walk to predict interactions. A paper mentions "J. Mol. Biol. (1981) 147, 195-197" to compare two...
View ArticleHow To Extract Max Score Blast Hit Among A Data Set?
Hi everyone, I performed a local blastp with a query protein vs 5 genome (ORF data ). Now i want to extract all the top 5 sequence automatically and make a final top hit file through awk/perl/shell....
View ArticleHow To Concatenate/Merge Blast Xml Outputs?
I process my blast (BLASTN 2.2.26+) searches through a script that divides the fasta inputs into N pieces, distributes one blast instance for each piece (in N processes), and, once over, concatenates...
View ArticleWhat Is The Algorithm Behind The Sequence Comparison In Uniprot Or In Any...
Hi, This is Shrujan, i wnat to know the algorithm behind the Sequence comparison in Uniprot or in any other database, which does BLAST. I need your valuable suggestions and guidance.Thanks &...
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 ArticleExtract 100 Downstream Sequence Of The Aligned Sequence Of Blast.
Hi all,I need to get 100 downstream of the nucleotide sequence from aligned results of the web blast query.Is there any way to get the required sequence from NCBI?
View ArticleGenomic coordinates from GI accession numbers
I have a list of GI accession numbers that I obtained following a protein BLAST search. These are from different bacterial genomes. I've pasted some examples below. 108765232 108769511 108769512...
View Articlehow to find different gene loci between two strains
I already have two complete genome,I want compare them to find different gene loci and related proteins.how can I do that?I read some papers about this,one said use blastp and then COGs,but I don`t...
View ArticleIs There A Query Parameter For The Online Blast That Would Filter For Hits...
Hello,I am running blastn, blastx and tblastx searches on NCBI's nt, est, nr and HTGS databases using transcriptome data containing ~56,000 contigs. I have been able to produce biopython scripts to run...
View Article