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11 votes
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BLAST(n): No hits found

There are three possible problems that come to mind. Masking Blast will mask low complexity regions by default. Since your sequence is nothing but Gs, it is a safe bet that it is being masked, so no ...
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10 votes
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Why does a very strong BLAST hit get lost when I change num_alignments, num_descriptions or max_target_seqs parameter?

I'm trying to figure out why. This will be a longer read, Tl;dr at the end: Doing a match There is a good match of Q against ...
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  • 391
9 votes

What is the difference between SAM mapping quality and Blast E-value?

The E-value and the mapping qualities are two very different things. The E-value is "a parameter that describes the number of hits one can 'expect' to see by chance when searching a database of a ...
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  • 952
9 votes
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Can't install newest Blast from Conda

I was able to reproduce your problem, even in a blank environment. ...
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  • 1,192
8 votes
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How to download the whole BLAST nt database into a specific folder?

-O is to specify the name of the output file. You want the -P option. So, from your example ...
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  • 1,806
8 votes
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Why is this makeblastdb command not working?

This looks like a bug in makeblastdb. Removing the final | | | from your sequence's description makes it work: ...
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8 votes
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How to extract fasta from a blastdb

You can extract fasta sequence from a blastdb constructed from a fasta file using blastdbcmd which should be installed when you install blast/makeblastdb. ...
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  • 302
8 votes
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how to set database other than nr for remote blast+ search

I believe you're looking for env_nr? It's listed as such, under Metagenomic proteins in the blastp webpage. It appears that the ...
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7 votes

Finding orthologues using BLAST on the NCBI database

BLAST is often a sensible way to find gene/protein homologs, but resolving those as orthologs vs paralogs etc. is a non-trivial task, especially when considering large numbers of species. Since you ...
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  • 3,527
7 votes

Randomness in BLAST

The Blast E is the expected frequency of obtaining false positive. This will depend on your query size (number of nucleotide or amino acid residues) and the size of the database. With a short query ...
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  • 504
6 votes

Why do BLASTn and prokka not seem to be searching the whole fasta file?

With a k-mer size of 28 it shouldn't be finding that many matches. And the prokka results are suspicious as well. Maybe you have multiple contigs (none larger than 100kb) in that file? What is the ...
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6 votes
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Possibility to save output blastn table in memory using biopython

You can specify send to stdout using out='-' in the Biopython wrapper. ...
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  • 749
6 votes

What kind of BLAST do I need to do to accomplish this task?

Clarification Just making sure - you have ~6000 datasets - one for each S.cerevisiae gene of interest - which are made up of homologues of each respective gene? And you want to filter out genes that ...
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5 votes
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Major variability in speed of BLAST between proteins

Try changing you evalue threshold to something like 0.001. If you blasted a sequence against a database containing 10,000 ...
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  • 166
5 votes

Randomness in BLAST

Sure, so you start out with what is called a bitscore, which is a normalized to the score calculated from the alignment between the 2 seqs which depends on the following equation. It is independent of ...
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  • 591
5 votes
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What are the different kinds of bioluminescent genes?

There are three processes wherein light is emitted. Bioluminescence: a chemical reaction releases light. The enzyme that does this is luciferase, while its substrate is luciferin, a small molecule. ...
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4 votes
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creating graph of distribution of blast hits on the query sequence

You probably want to include query start (qstart) and query end (qend) in your blast output. Something like this: ...
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  • 3,551
4 votes

Fast and reliable alternatives to blast

Besides generic nucleotide aligners, there are also more specialized tools for the alignment of 16S amplicon sequences, e.g. SINA (article, software) which is part of SILVA
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4 votes

Fast and reliable alternatives to blast

As I understand, the software tool Lambda is a viable, yet lesser known alternative to BLAST in the context of taxonomic classification of NGS data.
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4 votes

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

The answer is it depends. 40% pident with ~100% qcovs (assuming length of protein is not very small) tells you that the virulence factor (VF) and your prokka predicted protein are likely homologs, ...
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  • 3,527
4 votes

How is BLAST's nr database created?

The Refseq team and also the NCBI resource coordinators team publish a new paper every few years, so check out the many papers (e.g. here or here), but to answer your 2nd question, non-redundancy here ...
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  • 3,527
4 votes
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Software for taxonomic assignment?

You could take a look at kraken2 It should fit your purpose.
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  • 609
4 votes
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mpiblast alternatives?

The Diamond protein aligner is a very popular tool for pairwise protein alignment which is much faster than blastp while having comparable sensitivity. Diamond also supports the use of using multiple ...
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4 votes
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Assign multiple taxids to a sequence when constructing a local BLAST database

I inquired with the NCBI BLAST help desk today, and within an hour they provided a very helpful response. To summarize, when redundant records in the database are collapsed, the deflines (accessions + ...
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3 votes

How can I only get the species name for fasta sequences from blast results?

There might be a "cleaner" way to do this, but what I would do is first remove all of the spaces from the fasta sequence names and replace them with underscores using something like sed. ...
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3 votes
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assigning different characters to present and absent genes from blast output using perl or python

I wouldn't do this in Python, myself. This is a very simple text parsing problem and the standard *nix tools will be able to do it very easily. For example with awk:...
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3 votes
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Blast hits disappearing after changing -evalue

I am the author of the question / answer here Why does a very strong BLAST hit get lost when I change num_alignments, num_descriptions or max_target_seqs parameter? To my knowledge changing the ...
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  • 391
3 votes
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Transform traditional blast output to `--outfmt 6`

Biopython has a parser for Blast's default text format (which I assume is the one you have). Just use the blast-text string to specify this format in ...
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3 votes

Transform traditional blast output to `--outfmt 6`

The blast_formatter command allows you to produce output in any of the formats supported by BLAST. However, it requires that you run ...
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3 votes

Major variability in speed of BLAST between proteins

The evalue associated with a blast HSP (High-scoring Segment Pair) is a measure of how often you would expect to find such an HSP in a database of this size by pure chance. For instance, if you blast ...
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