Questions tagged [sequence-homology]

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

I need to find homologs of certain proteins by BLAST search or similar. But I want filter (select) homologs from organisms that are classified as thermophilic or hyperthermophilic. I am wondering if ...
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How to extract homologous sequence data from multiple .vcf.gz files?

I have short read data from multiple samples stored as scaffolds.vcf.gz files. I have some gene sequence of interest. I want to find the closest homologous sequence ...
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How to retrieve full-length sequences from hhblits output

I am using hhblits, part of hh-suite3. I am using it to query databases from the Soeding lab, such as BFD or Uniclust30. After having identified hits, could anyone tell me what they use to retrieve ...
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How to use multiple .pdb files as templates for homology modelling?

I just ran an AlphaFold job for PduK from the Pdu BMC operon and got very strange results including a large circular loop of random coil. According to Mayer et al., PduK should be semi-triangular ...
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Converting gene symbols between species

I have a list of genes in a mouse model How I can find the equivalent gene symbol/name for human from them? This is my list ...
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Can ortholog genes have different names among different species?

To be specific, we have different lineages of E. coli. I wondered if the ortholog genes among them should all have the same name in all lineages or can they also have different names?
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Finding 2000 bp sequences that occur more than once in the genome

I am looking for a software that can identify long sequences (1500-2000 bp) that occur more than once in my genome of interest. A k-mer counter like KMC could have worked, but KMC has a max limit of ...
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Comparing groups of 16S rRNA sequences - how to?

I have several groups of 16S rRNA sequences associated with taxonomic groups (let's call them A, B and C). The sequences within each group have a common ancestor and are on average more closely ...
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Analyzing proteins based on sequence similarity

Using NCBI Gene database, I retrieved list of 7015 protein which are implicated in autism pathogenesis. This list includes tax-ID, organism name, symbol, aliases, map location, chromosome, genomic ...
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1 vote
1 answer
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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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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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5 votes
2 answers
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How can I locate duplicated regions in a sequence?

I am facing an issue when trying to align short reads against a region in human chr5. The two Sensory Motor Neuron genes, (SMN1 and SMN2) are almost 100% identical and this causes the aligner to fail ...
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Protein SCA and DCA

Could you please suggest suitable R packages for statistical coupling and direct coupling analysis of protein sequences? I know there are Python packages for those: SCA and DCA. I was looking for ...
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Are gene names same across species?

I have a bunch of gene names of Apis mellifera (specifically 194). I used these gene names as an input on STRING database to create a network for Drosophila melanogaster. 54 of those genes were also ...
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4 votes
1 answer
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What does an output of -I for all amino acids mean in a psi-blast pssm matrix file?

I have run psi-blast using the NR database, remotely, with one iteration, for several sequences to calculate an evolutionary profile (PSSM) for each of those sequences. However, many of the PSSM ...
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7 votes
2 answers
550 views

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

I'd like to create a dataset consisting of all sequences which are either present in the PDB, or whose homolog is present in the PDB. In other words, any sequence in the PDB or any sequence related to ...
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  • 179
5 votes
3 answers
956 views

Obtaining all protein sequences with a particular domain architecture from Pfam

I want to get the alignment of chain A of 1kf6 (PDB ID) from the pfam database here. This protein chain has two main domains (FAD_binding_2 and Succ_DH_flav_C). In pfam there is a link to one of ...
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what is the difference between local identity and global identity for homolog finding?

We believe that if after running blast, the global identity between a resulting sequence and our query is at least 30%, we can say that two sequences are homologs. what is the difference between local ...
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1 answer
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Duplicate long hits from PSI-BLAST

I had a protein Refseq ID and I PSI-BLASTed this sequence against Refseq database. We all know that the Refseq is a Reference sequence database and it shouldn't have redundancy. After BLASTing my ...
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7 votes
2 answers
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Finding homologs of a protein sequence

I have a refseq ID of a protein from E.coli and I want to find homologs of this protein. I ran Blast against refseq database but I got a lot of sequences most of which were from Ecoli again. I decided ...
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6 votes
1 answer
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Detecting portions of human proteins with high degree of microbial similarity

I'm a newcomer to the world of bioinformatics, and in need of help solving a problem. My goal is to take a list of human proteins, and identify segments (13-17aa in length) with a high degree of ...
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