# 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 identity and global identity and how can we calculate them? the following file is the global alignment result of one of my PSI-BLAST hits against query:

Aligned_sequences: 2
# 1: NP_418577.1
# 2: WP_036312822.1
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 264
# Identity:      85/264 (32.2%)
# Similarity:   125/264 (47.3%)
# Gaps:          29/264 (11.0%)
# Score: 376.5
#
#
#=======================================

NP_418577.1        1 -----------MAEMKNLKIE-------VVRYNPEVDTAPHSAFYEVPYD     32
..|..:..|:       :.|::||||..|....|:|...

NP_418577.1       33 ATTSLLDALGYIKDNLAPDLSYRWSCRMAICGSCGMMVNNVPKLACKTFL     82
.|..:||||..||.::...||:|.||...||||..|.:|...:|||||.:
WP_036312822.     51 PTDRVLDALHRIKWDVDGTLSFRRSCAHGICGSDAMRINGRNRLACKTLI    100

:  |.:..:.|||:...|:|:||:|||..|.||...::|::...|.....
WP_036312822.    101 KDLDISKPIYVEAIKGLPLEKDLIVDMDPFFESFRDVQPFLQPKSAPEPG    150

NP_418577.1      131 GTNIQTPAQMAKYHQFSGCINCGLCYAACPQFGLNPEFIGPAAITLAHRY    180
....|:....|.|...:.||.|..|.::||.|..:.::.|||||..|||:
WP_036312822.    151 KERFQSIKDRAVYDDTTKCILCAACTSSCPVFWTDGQYFGPAAIVNAHRF    200

NP_418577.1      181 NEDSRDHGKKERMAQLNSQNGVWSCTFVGYCSEVCPKHVDPAAAIQQGKV    230
..||||.....|:..||.:.|||.|.....|:|.||:.::...||.:.|.

NP_418577.1      231 ESSKDFLIATLKPR    244
...:.
WP_036312822.    251 AVLRG---------    255

#---------------------------------------
#---------------------------------------
the following file is the local alignment of that hit against query:
Aligned_sequences: 2
# 1: NP_418577.1
# 2: WP_036312822.1
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 219
# Identity:      83/219 (37.9%)
# Similarity:   119/219 (54.3%)
# Gaps:           2/219 ( 0.9%)
# Score: 390.5
#
#
#=======================================

NP_418577.1       13 RYNPEVDTAPHSAFYEVPYDATTSLLDALGYIKDNLAPDLSYRWSCRMAI     62
|::||||..|....|:|....|..:||||..||.::...||:|.||...|
WP_036312822.     31 RFDPEVDAEPRWVDYDVEMYPTDRVLDALHRIKWDVDGTLSFRRSCAHGI     80

NP_418577.1       63 CGSCGMMVNNVPKLACKTFLR--DYTDGMKVEALANFPIERDLVVDMTHF    110
|||..|.:|...:|||||.::  |.:..:.|||:...|:|:||:|||..|
WP_036312822.     81 CGSDAMRINGRNRLACKTLIKDLDISKPIYVEAIKGLPLEKDLIVDMDPF    130

.||...::|::...|.........|:....|.|...:.||.|..|.::||
WP_036312822.    131 FESFRDVQPFLQPKSAPEPGKERFQSIKDRAVYDDTTKCILCAACTSSCP    180

NP_418577.1      161 QFGLNPEFIGPAAITLAHRYNEDSRDHGKKERMAQLNSQNGVWSCTFVGY    210
.|..:.::.|||||..|||:..||||.....|:..||.:.|||.|.....

NP_418577.1      211 CSEVCPKHVDPAAAIQQGK    229
|:|.||:.::...||.:.|
WP_036312822.    231 CTEACPRGIEITKAIAEVK    249

#---------------------------------------
#---------------------------------------

• BLAST (Basic Local Alignment Search Tool) doesn't give you global alignments, so you may need to reconsider what you're doing/asking. Furthermore, "homolog" has a very specific definition. Homologs are genes that are both descended from the same ancestral sequence. It doesn't, as many often mistake, mean 'similarity'. 30% sequence identity, does not imply homology by itself. You need more information. Jun 21 '17 at 8:49
• Take a look here (ebi.ac.uk/Tools/psa) if you want to find tools for local and global alignment. Jun 21 '17 at 8:50
• Perhaps I'm wrong but "They must have globally good identity" still isn't really enough to say that these sequences are homologs. You need ancestry information for the organisms you're interested in. If you really want to know orthology/homology, I'd suggest using a dedicated orthology finding program like OrthAgogue, OrthoMCL, or better yet ROARY if your sequences are bacterial. Jun 21 '17 at 9:04
• No they don't. It all depends on how closely related the species are. Please edit your question and add more information. There is no magix sequence simlarity threshold that defines homology. Jun 21 '17 at 9:04
• There is no magic formula. For closely related species I would expect a sequence identity of far more than 30% for a true homolog but for distant species, I could also expect far lower. As I told you in my answer to your previous question, it is far more important to look at the conservation of specific residues than to look at the overall sequence similarity value. Jun 21 '17 at 9:15