10 votes

Are gene names same across species?

Gene names are not consistent across species. Most of the time genes are automatically annotated and the algorithms try to give names that are similar to their matches in other organisms, but not ...
  • 12k
5 votes
Accepted

Finding homologs of a protein sequence

It depends on what you're looking for. If you're just looking for sequence homology, then you can simply pick the best hits from a blast search. If, however, you are referring to functional homology, ...
  • 8,235
4 votes
Accepted

Are gene names same across species?

You could try using BioMart in Ensembl Metazoa. Filter by your list of gene names in honeybee, then get the fly homologues as attributes. The homologues are calculated by sequence comparison and ...
4 votes

How to get all PDB homologs from Uniprot (mapping + BLAST)?

For the correspondence between PDB and Uniprot entries you can use SIFTS -- a semi-automated mapping between PDB and UniProt maintained by PDBe. The pipeline that creates the mappings uses BLAST and ...
  • 1,091
4 votes

Finding homologs of a protein sequence

It sounds like Smart BLAST might do what you want. Here's the description of it's goal: SmartBLAST is a new and experimental NCBI tool that makes it easier to complete common sequence analysis ...
  • 12k
4 votes
Accepted

Detecting portions of human proteins with high degree of microbial similarity

Sounds like precisely the job BLAST was developed for. Now, which flavor will depend on what you want to do and what data you have available. Some options: PSI-BLAST: this is usually the best choice ...
  • 8,235
3 votes

Converting gene symbols between species

Easiest way is BioMart. Help video to get you started here. Use the mouse genes dataset and filter by the list of gene names, get the mouse gene name and the human gene name (listed under homologues) ...
3 votes

Can ortholog genes have different names among different species?

Gene naming is pretty subjective and even a single gene can have many names. If you're lucky orthologs will be named the same in different lineages, but you can't rely on it. Better to use gene ids (e....
  • 3,577
3 votes
Accepted

Finding 2000 bp sequences that occur more than once in the genome

MUMmer includes a repeat-match tool which can do exactly that: ...
3 votes

How to identify [hyper]thermophilic proteins by BLAST search?

It seems like the main issue is finding a list of species to filter your blast results on. I will therefore address this list of species issue. There are some resources such as Microbe Directory that ...
3 votes

Protein SCA and DCA

While my suggestion doesn't technically fit your qualifications, I do think it may be useful. I bring this up because you mention you want to continue with your R workflow. I am assuming you don't ...
  • 1,129
3 votes
Accepted

what is the difference between local identity and global identity for homolog finding?

If you want a purely alignment based approach to begin to infer homology (note I say infer, as we stated in the comments, this isn't sufficient to say 2 sequences are homologs), I would use a Multiple ...
3 votes

Obtaining all protein sequences with a particular domain architecture from Pfam

An alternative way is using the Hmmer website, and do a hmmsearch with the Pfam accession, forex. (PF02910). Navigate to the domain tab and find the domain architecture that you are interested in and ...
2 votes
Accepted

Obtaining all protein sequences with a particular domain architecture from Pfam

I believe you can do this using SQL files of the database. First you need to get the integer accession of this architecture. architecture table has the following ...
2 votes

Obtaining all protein sequences with a particular domain architecture from Pfam

That does not appear to be possible using PFAM. I would suggest trying a different database. I managed to perform the same query using SMART (http://smart.embl-heidelberg.de/), via entering "Pfam:...
2 votes
Accepted

Duplicate long hits from PSI-BLAST

This is what is known as a feature, not a bug. Note that your identical proteins all have accessions starting with WP_. These are special "non-redundant ...
  • 8,235
2 votes

How can I locate duplicated regions in a sequence?

GeneBlocks is a Python library for comparing DNA sequences. It can be used to find common blocks (identical regions) in a group of DNA sequences. Using a modified version of your example (I duplicated ...
  • 2,584
2 votes

How can I locate duplicated regions in a sequence?

If you know approximately where are the duplicated regions, you can cut them out from the genome and align the two block using tools like MUMmer or Mauve. Although Mauve is not scalable solution (You ...
2 votes

Analyzing proteins based on sequence similarity

I suggest you give DAVID a try. Specifically, their Functional Annotation tool. Just enter your list of protein IDs, and it will return groups of proteins where particular GO functions are ...
  • 8,235
1 vote

How to identify [hyper]thermophilic proteins by BLAST search?

Warning: Hearsay As the others have said, filtering by a list of taxonomy ids is the only one. However, there is one extra consideration if this is for wet lab applications: expression yields even ...
  • 3,854
1 vote

How to use multiple .pdb files as templates for homology modelling?

AlphaFold2 You are asking about how to hybridise different threaded models, but I would not give up on AF just yet as it can do complexes. AlphaFold2 is conceptually amazing, but does have some issues ...
  • 3,854
1 vote
Accepted

Comparing groups of 16S rRNA sequences - how to?

If you want to make an all vs all with blast this can be helpful. You can create a blast database with your sequences and then search against itself. ...
  • 759
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 ...
  • 759
1 vote
Accepted

What does an output of -I for all amino acids mean in a psi-blast pssm matrix file?

It means -inf. It has to do with how the PSSM score is calculated.
  • 3,551
1 vote

How to get all PDB homologs from Uniprot (mapping + BLAST)?

You can download a BLAST db containing all sequences of proteins in Uniprot and in the PDB. The way I would go about this is first download the databases for uniprot and PDB, then query the PDB ...
  • 201
1 vote

what is the difference between local identity and global identity for homolog finding?

Defining homology isn't as simple as an identity cutoff, however, you're right that homology seems likely given a certain identity. This is where e-value comes into play. See: https://en.wikipedia.org/...
  • 602

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