Questions tagged [sequence-homology]

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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 ...
1
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1answer
31 views

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 ...
1
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0answers
17 views

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 (...
3
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1answer
196 views

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 ...
3
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1answer
147 views

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 ...
7
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2answers
120 views

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 ...
4
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1answer
94 views

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 ...
7
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2answers
355 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 ...
5
votes
3answers
591 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 ...
3
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2answers
371 views

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 ...
5
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1answer
86 views

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 ...
6
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2answers
1k views

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 ...
6
votes
1answer
76 views

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 ...