6
votes
How to determine a protein's cellular location based on its sequence?
You could use Blast2go to find the predicted relevant gene ontologies of your sequences. If you look for the cellular compartment sub ontology you should find the location of such protein. I have ...
- 4,721
5
votes
Accepted
blastp option to compare with a personal database
You can use these options:
blastp -query my.faa -db VFDB.fas \
-perc_identity 50 -outfmt 6 \
-evalue 10e-5 -out results.txt
Then select the 5th ...
- 769
5
votes
How to export web NCBI tBLASTn results in table format with many queries?
It sounds like your easiest option is to just install blast on your local machine and set up the databases there. It really will only take a few minutes to blast 6,000 sentences against a yeast genome ...
- 3,201
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, ...
- 3,968
3
votes
Comparing sequence similarity of two sets of peptide sequences?
Not sure what is the shortest peptide one can fish out with LAST out of small protein database (well, it starts with protein FASTA file), but you may check out LAST ...
- 398
3
votes
FASTA and PDB: How to specify chain?
The NCBI BLAST can be used with the PDB DB (which NCBI has). The PDB codes are stored as 4 letter codes underscore chain, e.g. 1GFL_B. The catch is segment ...
- 4,274
2
votes
How to determine a protein's cellular location based on its sequence?
You can run the sequence through tools like SignalP to look for cell surface signals and so on, which will give you a clue about where I is bound for.
None of these tools will give you an absolutely ...
- 335
2
votes
Blastp MSA to the same length
BLAST isn't appropriate for multiple sequence alignment.
BLAST generates pairwise alignments. Furthermore, the aligning regions shown in a BLAST report only include subsets of the hit sequences.
To ...
- 146
2
votes
Comparing sequence similarity of two sets of peptide sequences?
I would suggest focusing on short k-mers if you are using very small sequences. Simply quantify the similarity of the k-mer profile of each relevant pair of peptides. There are many tools for ...
- 4,252
2
votes
Accepted
makeblastdb creating multiple files of unexpectedly large sizes
Welcome to the Bioinformatics site! Hopefully you find the below helpful.
Regarding the creation of a RefSeq protein database locally...as you mentioned, there are pre-made RefSeq BLAST databases ...
- 782
2
votes
Given a FASTA file with a set of genes, how do I determine that set's conservation among a genetic order?
It's possible that MOLE-BLAST could help for you:
MOLE-BLAST is an experimental tool that helps taxonomists find closest database neighbors of submitted query sequences. It computes a multiple ...
- 15.1k
2
votes
How to blast UniProt/RefSeq database from local clusters?
If an intermediate requirement is "do thousands of BLAST searches", the question is almost always an XY problem, i.e. asking about the attempted intermediate solution rather than your actual ...
- 15.1k
2
votes
How to blast UniProt/RefSeq database from local clusters?
The standard tool for this is NCBI's blast+ package. It is installable on most systems, and should be in the repositories of your distribution if you're using Linux.
Once installed, you can use it to ...
- 10.6k
1
vote
Comparing sequence similarity of two sets of peptide sequences?
After more search, I go for blastp-short with MHC peptides as query and my full-length proteins as database. Please share if you think it has problems.
- 329
1
vote
How are BLAST record scores calculated in biopython
The results you'd get are the same as with any other NCBI BLAST+ tools, python does not compute it.
Biopython can run a blast query qblast on the internet or ...
- 111
1
vote
Number of collinear genes are zero while running MCScanX
I'm not familiar with the MCScanX tool, but I see two potential issues that are worth investigating.
The cyp_dan.gff file does not look like GFF or any of its ...
- 5,110
1
vote
Accepted
How to BLAST a protein against a large set of organisms?
My solution is simply.
perform a web-based Blastp using the following parameters:
most dissimilar
5000 hits (maximum limit)
Restrict to Archaea (which is what you samples appear to be)*
If you hit ...
M__♦
- 13k
1
vote
How to BLAST a protein against a large set of organisms?
In the interface of blastp, you can limit the search space to organisms you want to. Yo can do this by introducing name species or Tax IDs, you can add more than one, but I bet you don't wanna ...
- 857
1
vote
How to get full alignment output from BLASTP?
Hmmm, firstly can you attempt multi-threading on a remote command via -num_threads 8...
...
M__♦
- 13k
1
vote
Accepted
How to do BLASTP for short sequences (<20 aa) effectively?
You should increase the -evalue 10 default option to a higher value because this value it's adjusted to the sequence database size. Check this table, maybe this can ...
- 769
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