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Questions tagged [blast]

The Basic Local Alignment Search Tool is a widely-used tool for finding and evaluating DNA or protein sequences. Users can utilize either their own sequences or the genomes of hundreds of organisms. It can be found at http://blast.ncbi.nlm.nih.gov/Blast.cgi

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Is it PSI-BLAST or BLASTP if I use PSI-BLAST for only one iteration

In my case, I used PSI-BLAST in the local BLAST+ to search queries against the self created database. After the first search, I added the searched result to the database and then conducted the ...
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32 views

Why do the RNAseq reads map to only a certain region of a viral genome?

I am looking at RNAseq data and mapping them to 3 RNA segments from Cucumber Mosaic Virus. I trimmed the adapters from the fastq files and converted them to fasta, which I searched against a virus ...
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8 views

What parameters of a blast file are appropriate to detect the real positives

I am analyzing the NGS results. I don't know what parameters of a Blast file I should choose to filter the positives: ...
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23 views

Does diamond tblastn exist?

I actually want to use diamond instead of blast because it is faster with small sequences and big genomes, but I actually want to make a tblastn with several protein sequences as queries and the ...
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62 views

How to determine which is the nucleotide sequence of a gene?

I have came across a few genes that show different nucleotide sequence in different databases. I then found out that the sequences are actually reverse complement of each other. How do i determine ...
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259 views

What direction is a sequence in databases written?

In many databases, the DNA sequences for proteins are given as a string of a,t,g,c without specifying whether the starting is from 5' or from 3'. Also it is not specified if it is the coding or non ...
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66 views

Why are the results of local BLAST and miRbase BLAST different?

I am trying to reproduce locally on my computer what I get running mirbase on their website using BLAST. The search sequences is: mature miRNAs which I had downloaded on my computer and make it as a ...
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147 views

Blast databases

I am helping a colleague setup a local blast server. My background is computer science so I apologize if I use incorrect terminology. Using the NCBI blastn webpage, one of the databases listed is "...
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2k views

Alternatives to NCBI BLAST during US government shutdowns?

Many molecular biologists are used to going to NCBI BLAST for quick, hassle-free BLAST searches of their genetic or protein sequences. However, during the last American government shutdown in 2013, ...
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How to selectively filter BLAST results for an endogenous retroviral LTR to retrieve members of the same ERV family?

I'm running a local BLAST search on a HERV-K(HML2) LTR sequence in the human genome. I get thousands of hits. I want to retrieve the hits that correspond to other HERV-K(HML2) LTR sequences only. ...
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134 views

How do I download entire human genome for local blast formatting and searching?

I'm trying to make a copy of the entire human genome for local blast queries on my machine. I understand that I need to download it from the NCBI FTP server here... ftp://ftp.ncbi.nih.gov/genomes/...
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38 views

Can conventional PCR amplify DNA from different organisms from a specimen in a single step?

I've understood so far that in conventional PCR, the most abundant DNA/genotype present in the speciment at the beginning of the reaction is selected and esponentially amplified. So that cPCR are ...
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390 views

Lactobacillus casei and paracasei

I am carrying out a study of lactobacilli isolated from different samples. Genus and species are identified using a sequenced 1000pb long 16S fragment in BLASTn. I cannot distinguish between L. casei ...
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254 views

Multiple transcripts matching same gene in de novo assembled RNA-seq data, but FPKM values vary?

I have a data set of de novo assembled RNA-seq datasets across different sample types. When BLASTing, many of the matches of the individual transcripts match to the same gene on the reference genome. ...
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33 views

Creating BLAST database with nucleotide “place holder”

I have a set of nucleotide sequences that contain some special characters with multiple meanings: H -> C, A or T K -> G or T M -> C or A R -> G or A S -> C or G W -> A or T Y -> c or T I would like ...
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560 views

What is the relationship between the e value reported by HMMER and BLAST? (Are they equivalent?)

Both HMMER and BLAST report an e value for alignments. Is it calculated in the same way and - assuming that default settings are used - can they be compared directly (are the equivalent)? If not ...
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BLAST protein sequences from 2 different bacterial species

I am interested in finding a consensus sequence of a protein found in e.coli, in Pseudomonas aeruginosa. I am using pseudomonas.com to BLAST p the amino acid sequence of the protein that i have found ...
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6k views

What is the meaning of “E-value” in the BLAST search?

After reading many pages, I still do not understand the definition. Can someone use simple words to explain me that? https://en.wikipedia.org/wiki/BLAST This expectation or expect value "E" (often ...
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1answer
85 views

How to conduct PSI-BLAST for a given protein sequence against bacterial protein database only?

I have a list of 100+ proteins and I need to conduct psi-blast for each one of them against "bacterial proteins" only. I went to NCBI's protein blast tool, but couldn't figure out how to select/limit ...
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39 views

Merge NCBI and Ensembl data

Apologies if this is a really naive question, but I cannot figure out how to do this easily. Here is a related post regarding the best method to find orthologous genes of a species. Let's say I have ...
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5k views

Scoring matrices (BLOSUM & PAM) in BLAST and other sequence-comparison programs

The Wikipedia page on BLAST states that: The scores are created by comparing the word in the list in step 2* with all the 3-letter words. By using the scoring matrix (substitution matrix) to score ...
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3answers
255 views

BLAST with minimum E-value cutoff

It's easy to set the maximum E-value threshold in a BLAST request. I need to set the minimum E-value. Does anybody have any suggestions?
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88 views

How to restrict a BLAST search to include only a few protein sequences?

I am performing a BLAST search and I need to filter the output to a certain family of proteins. Specifically, I need to get matches within the CYP152 family of the Cytochrome P450 proteins. I can ...
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2k views

Why does BLAST reduce word size for short proteins?

I'm using BLAST to identify a short protein (BLASTp). If I check the short query then the word size reduces from 3 to 2. However the search will then be less ...
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71 views

My BRIG run is suspiciously quick. What is a typical length of time for a run?

I use the BRIG (BLAST Ring Image Generator) program to compare prokaryote genomes. It executes a local BLAST+ and visualizes the results as rings around the reference genome. I downloaded three ...
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1answer
110 views

why does the score matrix influence the E value (BLAST)

When I align two HBB protein sequences wich have 80% identity, I used two kind of score matrices: Blosum62 and PAM30, to figure out the impact on my results. I noticed that the bit score is higher ...
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706 views

How is e-value calculated in BLAST 2 sequences (BLAST+)?

In the BLAST+ packages, you can align two sequences instead of searching a database: tblastn -query seq1.fa -subject seq1.fa The web BLAST documentation states ...
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493 views

Why are sequencing reads shorter than PCR products?

I have desinged and tested primers for RT-PCR, then purified the PCR products from the gels and send them to sequence at GATC (SUPREMERUN) using the forward primers. After blasting the reads to ...
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653 views

BLAST(Basic Local Alignment Search Tool) is heuristic?

How can we say that BLAST is based on a heuristic algorithm, as after finding one common word in the query sequence and a database sequence it performs pairwise alignment by dynamic programming - ...
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326 views

Basic Local Alignment Search Tool (BLAST)

Why would BLASTP (Basic Local Alignment Search Tool) be a poor tool to search for motifs in protein sequences?
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90 views

Do the BLAST scores have any relation between them?

Is there any relation among the BLAST scores (E-value, similarity, identity, gap, bit score)? Is the e-value score for an alignment proportional to other scores, such as similarity score (i.e. the ...
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1answer
248 views

How to Determine the Most Conserved Sequence from BLAST Result?

I used BLAST to find the best aligned DNA sequence to my query sequence. The BLAST result shows a number of sequences that it calculated to be the best aligned sequences to the query sequence that I ...
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1answer
366 views

blastn: What substitution matrix is used?

I'm currently working aligning sequences, and I need to compute similarity between pairs of DNA 'words' of a particular length. For amino acids I am able to use the substitution matrices in Biopython ...
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2answers
816 views

How to remove duplicate results from BLAST?

If I run BLAST using a protein sequence (e.g. human p53), I get many matches to the same protein, presumably from different research projects. As you can see from the screenshot, all are similarly ...
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132 views

Primer Design with Primer-BLAST over specific site

I am trying to design primers using Primer-BLAST such that the forward primer spans a specific base pair site. I am looking at KRAS for which I believe the RefSeq ID is NG_007524.1 and the forward ...
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275 views

Determining the percentage of the query of an alignment from a BLAST output

Given this BLAST output, how can I determine the percentage of the query sequence in the alignment? I know that it's also referred to as 'query cover' but I can't seem to find anything online that ...
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318 views

Primer Design With Primer-BLAST

I am trying to design primers for sanger sequencing snp detection. In the past I have used Primer-BLAST, but I'm trying to pick up KRAS codon 12 mutations. The problem is that in Primer-BLAST you ...
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1k views

How to get only perfect matches with blastn? [closed]

I have installed Blast locally and I've configured the nucleotide database to use. I want to search some sequences (from a .fastafile) in this genome. So I used blastn: ...
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2answers
152 views

Aligning multiple sequences in heterogeneous group

I have a list of ~200 DNA sequences, representing probably 50 different genomic regions but they're all mixed up. For example, if I have seq1, seq2.... seq10, ...
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1answer
590 views

what the best E-value cutoff in the miRNA homology search

I'm trying to use miRBase database to annotate some microRNA sequences in length 22-24bp. I highly appreciate if someone let me know whether I should do this BLAST against mature miRNA or stem-loop ...
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1answer
909 views

Find protein homologs with BLASTp

I'm trying to find homologs of a set of proteins using BLASTp. I'm working with custom databases. I'm using evalue of 0.00001 as threshold. I would like to filter queries having hits with >90% ...
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2answers
805 views

Local BLAST Copy Number per Hit

I generated a series of local BLAST databases using makeblastdb of metagenomic data and am searching for the presence of a particular gene. While I can do the normal BLAST analysis looking at e-values,...
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1answer
47 views

programmatic fast search of 100-1000 short reads to a public server and obtain list of nearby genes

What are the options for programmatic fast searching of 100-1000 short reads to a public server and obtain list of nearby genes where the reads map? Input: ~100-1000 short reads Output: GFF list of ...
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1answer
112 views

BLASTn vs ORF tools

Sequencing projects sequence one strand and call that the + strand and then extrapolate the sequence of the - strand. This means that sometimes the genomic sequence that you download from a database ...
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1answer
48 views

Why are different lengths of nucleotides taken for structure prediction from an miRNA match area after BLAST analysis?

Generally in miRNA prediction most researchers do as Blast search with a set of miRNAs downloaded from miRBase with the parameters they require. Later on usually custom methods are utilized to get an ...
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1answer
1k views

The parameter for setting the number of mismatches in standalone blast

In a standalone blast search, is there a parameter that could be specified to fix the number of mismatches allowed in an alignment. I went through the parameters and I could only find parameters to ...
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2answers
811 views

Primer design and BLAST E value stringency

When searching for misprimings I have been told that an e value that is higher than 0.01 is ok and will produce no significant amounts of mispriming. Yet I searched some and it would seem that the e ...
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2answers
316 views

How do you find pre-miRNAs from mature miRNA Blast output?

So in short, I did a blastn with standalone blast using all known miRNAs against the EST sequences in a genome (word length 7 and e-value 0.01). Now to confirm one of the next steps would be obtain ...
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2answers
686 views

GO terms for non-model organisms

I have a list of differentially expressed genes from an RNA-Seq experiment in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I have ...
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3answers
839 views

Is there a PSI-BLAST for nucleotide sequences?

I understand that one can translate a nucleotide sequence and run PSI-BLAST on the protein (proteins if you take the 6 reading frames), but I'm looking for distant homology for bacterial small RNAs (...