Questions tagged [blast]

Basic Local Alignment Search Tool: algorithm that finds regions of similarity between a pair of sequences, can be used to query an unknown sequence against a database of known sequences.

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32 views

how to have a blast xml file in a readable and understandable way

I got a blast xml file after a DNA sequence search. The XML file is not very readable. What is the way to make it more understandable? This blast contains about twenty matches. Here is the xml file
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How to download taxonomy table from blast ncbi?

After doing a blast analysis, at ncbi's platform, I received the taxonomy table like one showing below. I would like to download this table. There is no command available from the platform. Copy and ...
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1answer
52 views

Do you know a program/script to count how many sequences have mismatches on each position of my primers?

I'm working with primer analysis and design, and so far I've performing it in Excel but: a) I don't like Excel, b) I do it manually, c) I don't like Excel, d) it gets tedious when working with ...
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19 views

Command-line blastn not responding; trace says “Resource not available”

I hadn't used the NCBI command-line tools for a while, and just got back into it. But no matter where or how I run blastn now, I get an almost complete lack of response: just the initial "BLASTN ...
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25 views

BLAST, last step: Needleman-Wunsch + S-score

In my bioinformatics course we studied the BLAST agorithm. After finding the HSP's and joining the HSPs together that are close enough and in a correct diagonal trend, we perform a next step: namely a ...
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15 views

Getting BLAST to show similar sequences outside of a specific protein family

I'm trying to build an alignment of proteins in the major facilitator superfamily (MFS). I have alignments of a family of peptide transporters, the SLC15 family, but I would now like to extend the ...
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1answer
71 views

Blast results filters

I performed a blastn search of NGS data against ssRNA database download from Internet, with a expected value 10-4. The size of NGS data reads is of 125 bp. I have analyzed the blast results of the ...
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1answer
19 views

Standalone Blast+; Automating searches, Blastn formatting, interpretation

I am struggling with using NCBI's standalone blast, particularly the blastn feature. I have a large number of nucleotide sequences that I want to use blastn to ID. The goal is to retrieve information ...
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38 views

Analyzing a blast result of NGS data

I am analyzing BLAST results from total RNA NGS, pair ends. This BLAST results was performed against the ssRNA virus database download from NCBI. I filtered those read data whose paired ends ...
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20 views

Why is the output from the online DISOPRED portal and a local DISOPRED installation different?

I recently installed DISOPRED on a computer cluster to predict the intrinsic disorder in long (~800 residues) amino acid sequences. I followed instructions provided on an online blog, since I couldn't ...
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1answer
26 views

Can you give me a detailed explanation about PrimeBlast?

I am trying to write a research paper on PRIMER-BLAST. I have read something about it on https://www.ncbi.nlm.nih.gov/pubmed/22708584/ but still, it is not enough. So can you please tell me more ...
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how could i find uniprot ac in blast?

I have made a search in p-blast. I would like to search for the protein results in uniprot. how can I do it directly? I can go to GENBANK but i would like to go to UNIPROT. Thank you!!!
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Primer-Blast Custom Database [error]

I'm using Primer-Blast to compare a PCR template against a custom database of reference sequences, using Primer-Blast's Custom database functionality. However whenever I try to upload a FASTA file as ...
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1answer
14 views

how can i search in p-blast against UNIPROT(not only swissprot)

i need to search for one protein against UNIPROT in BLAST for a selected organism. How can I do it? (SWSISSPROT+TREMBL) THANKS!!
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phmm blast hmmer

i have created a phmm in hmmer from a multiple alignment focused on E. coli produced in tcoffee from sequences taken from blast similar to my query sequence. I would like to ask how i can compare the ...
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BERT Language Model and Gene Sequences - How Do I Relate Clusters of Sequences?

I hope you'll indulge a question from a computer scientist with limited bioinformatics knowledge. I've been working with the Google tool for language modeling called BERT. It's generally regarded ...
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34 views

Cannot blast against specific NCBI databases

I am having issues with some prokaryote reference genome databases (exact names : ref_prok_rep_genomes.*), that I downloaded from the NCBI website : https://ftp.ncbi.nlm.nih.gov/blast/db/. Files in ...
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1answer
58 views

Possibility to save output blastn table in memory using biopython

Is there a possibility, using biopython to save output table of blastn in memory, not in file on hard drive, for process it using pandas for example and then delete it from memory? I mean, is there a ...
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1answer
41 views

How to do BLASTP for short sequences (<20 aa) effectively?

I am trying to find sequence homology between viral sequences and my protein of interest. I have the sequences of their epitopes which varies from 5 to 500 amino acids long. For shorter sequences, it ...
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1answer
132 views

Cannot blast database created with blastdb_aliastool: BLAST Database error: No alias or index file found

I want to merge/concatenate BLAST databases as suggested here. This is my example script that explains what I'm trying to achieve better than words can: ...
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1answer
43 views

Translating a genome sequence into possible frames

I have a sequence below from MYC gene about which I need to translate the sequence in all possible frames AND identify (for each frame) which codons are actually used in MYC ...
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1answer
36 views

how to generate structure file from blast results of an input sequence

I have tried to incorporate blast in my application using biopython.i could extract the blast results but now i want to extract the structure file corresponding matches. My code is : ...
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200 views

What are the different kinds of bioluminescent genes?

I know of the common green glow gene but I forgot the name and I also know that some algae glow blue. There are so many types of bioluminesent organisms, so I am wondering what species have which ...
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43 views

Is there a “definitive” database for Mobile Genetic Elements?

This isn't quite my speciality, but I've been tasked with finding any evidence of Mobile Genetic Elements (like transposable elements, retrotransposons, bacteriophages, etc.) within some WGS samples. ...
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How can I find genes of fundamental metabolic processes for an organism?

I want to find genes of fundamental metabolic processes in the Phytophthora cinnamomi genome. I'm using the genome sequence deposited in the NCBI and I'm searching ORF by ORF, using the ORF finder (...
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3answers
41 views

How to find a homolog that has a PDB structure available

I tried to find a homolog that has a PDB structure available so I can use this PDB file for comparative modeling. I ran a BLAST search but none of the search results seemed to have a known structure. ...
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Pfam search using hmmer but only for a specific taxonomy

I am trying to do a de novo assembly using Trinity. Using Transdecoder and blastp/hmmscan search to do annotation (using Uniprot/pfam databases). https://github.com/TransDecoder/TransDecoder/wiki . ...
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1answer
327 views

Interpretion of my coronavirus 2019-nCov, Wuhan, China BLAST tree?

This is the BLAST tree of the latest coronavirus out of China. It seems strange that there is so much divergence from all the other coronaviruses. Is this expected of new diseases?
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How to confirming exon shuffling from genomic sequence, promoter sequence, and mRNA sequence?

I have the genomic sequence, promoter sequence, and mRNA sequence for a novel gene. It is thought that the gene is derived from exon shuffling of multiple genes. How do I characterize each of the 3 ...
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1answer
111 views

which NCBI tool is optimized to identify a species from a DNA fragment?

“The Iceman” was a man who lived 5300 years ago and whose body was recovered from an Alpine glacier in 1991. Some fungal material was recovered from his clothing and sequenced. Ice man : found as a ...
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59 views

TBLASTN error: Too many positional arguments

I was running tblastn using standalone blast2.9.0+ through Ubuntu Linux, to get the alignment result of a list of protein sequences for same species, against its complete genome file. The command I ...
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1answer
128 views

Is there any tool for fuzzy sequence matching?

Note: this question was also asked on biostars are you aware of any tool that is able to perform error-tolerant pattern-matching search on protein FASTA files? For example, I want to know, which ...
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1answer
89 views

blast nt vs Genbank

What is the difference between these two databases? ftp://ftp.ncbi.nlm.nih.gov/blast/db/ and ftp://ftp.ncbi.nih.gov/genbank/ I understand that BLAST database has both nt for nucleotide and np for ...
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1answer
83 views

Plotting distance tree from blastn output

I'm trying to plot a simple distance tree of my blastn output with nj (like the tree view on NCBI). From what I understood, what I think I should do is extract all the hsps from each alignment re-...
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1answer
79 views

Appropriate tool or algorithm for sloppy alignment of degenerate bases

I have an optimization problem where I have a degenerate nucleotide sequence I want to align against subsets of a reference genome (exons, specifically, to make the problem more tractable). The ...
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1answer
33 views

Huge variability in blastn speed between same short sequence job

I have been running a couple of blast searches and I am very suprised and somewhat frustrated by the huge variability in job completion time. The specifics of my blast search are as follows: Running ...
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30 views

BLAST server download

I discovered that Phytozome's BLAST results look quite nice (please see below). By any chance, does anyone know where to download this BLAST server in order to install it locally for organisms which ...
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1answer
100 views

blast command line

I would to use blastx from command line to analize a library produced with RepeatScout in format .fasta to find new transposable elements. I use this command ...
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2answers
336 views

How is BLAST's nr database created?

Is there a paper or web page describing the procedure for creating the nr database used by NCBI's BLAST implementation? I presume it's some type of clustering, but I'm curious about how exactly ...
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1answer
59 views

Alignment for predicting DNA hybridization?

I am currently working on a Computer Science project where we are trying to build a large set of orthogonal single-stranded DNA sequences. The goal would be to ensure that when put in solution, the ...
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1answer
145 views

How to filter blast results from blast run against virulence factor database

I downloaded virulence factor database from here , to predict virulence genes from few genomes that my lab sequenced. I performed local blast on the database with default setting and found around ...
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1answer
116 views

Merging / Concatentating BLAST Databases

I was wondering if any one has had success merging BLAST databases from multiple references? For a concrete example I have hg19 and a bunch of viral and bacterial genomes that all have been index ...
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1answer
242 views

taxon exclude list for searching local blast database using blastn

I am looking for a solution to exlude certain entries when searching a local blast nt database (with blastn), specifically the sequences from uncultured / environmental samples, ideally using their ...
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How to retrieve the best-scoring Trinity isoform from blastx results

I'm working on a somewhat unusual transcriptome focused on a killer X chromosome. This chromosome has some new genes, with expression levels quite different from their autosomal paralogs. I've found ...
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1answer
133 views

Hits in Primer-BLAST not found with programmatic blastn query

Summary: I'm writing an automated tool for designing Sanger sequencing primers (other tools don't do exactly what I want) that will be incorporated in a production diagnostic laboratory for on-demand ...
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3answers
112 views

Randomness in BLAST

So if you see the BLAST parameters it says The Expected value E is a parameter that describes the number of hits one can "expect" to get by chance when searching a database of particular size. It ...
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3answers
1k views

How BLOSUM Matrix is constructed and calculated

I would like to ask how BLOSUM matrix is constructed and calculated ? I read the wikipedia and I still do not understand it. I do not understand the mathematical calculations as I have low knowledge ...
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4answers
220 views

How to get the longest fasta sequence including all possible switching isoforms of a gene out of isoforms

I am working with RNA-seq data without a reference genome/transcriptome and am instead using a Trinity de novo transcriptome assembly. I analyzed both isoform and gene expression abundances using RSEM....
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1answer
767 views

Can't install newest Blast from Conda

I have run into an odd situation, where Anaconda repo page clearly states that the newest version of Blast in Bioconda channel is 2.7.1, however the version Conda wants to install (command ...
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5answers
662 views

Fast and reliable alternatives to blast

After some unexpected results (and previously reported) I heard that there are other tools for finding similar sequences besides blast that are faster and more accurate. I only found hmmer, but I don'...